> From: amber-request.ambermd.org
> Subject: AMBER Digest, Vol 541, Issue 1
> To: amber.ambermd.org
> Date: Thu, 13 Jun 2013 12:00:01 -0700
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: ntt=2 on gpu (Ross Walker)
> 2. Protein leaving periodic box (Hailin Huang)
> 3. Running MD NPT Ensemble Error (Benjamin Grant)
> 4. Re: Protein leaving periodic box (Daniel Roe)
> 5. bad atom type: N3 (In MMGBSA decomp calculations) (Jason Slingsby)
> 6. Step by step tutorial to using Ptraj in generating DCCM
> (#YIP YEW MUN#)
> 7. Unknown redidue when using tleap (Dongshan Wei)
> 8. Re: csh problem (David A Case)
> 9. Re: parameters of ions for TIP5P water box (Xioling Chuang)
> 10. Re: Unknown redidue when using tleap (ET)
> 11. Re: Running MD NPT Ensemble Error (ET)
> 12. Re: Running MD NPT Ensemble Error (ET)
> 13. Re: Unknown redidue when using tleap (FyD)
> 14. MPI Compilation problems Amber 12 on CentOS 6.2 (Frank Thommen)
> 15. glycame06_carbohydrate_hydrogen bond pattern (Rasha Alqus)
> 16. Re: glycame06_carbohydrate_hydrogen bond pattern
> (Karl N. Kirschner)
> 17. Re: MPI Compilation problems Amber 12 on CentOS 6.2 (David A Case)
> 18. Re: MPI Compilation problems Amber 12 on CentOS 6.2
> (Frank Thommen)
> 19. Re: MPI Compilation problems Amber 12 on CentOS 6.2 (David A Case)
> 20. Re: MPI Compilation problems Amber 12 on CentOS 6.2
> (Frank Thommen)
> 21. Re: Unknown redidue when using tleap (Dongshan Wei)
> 22. Re: Step by step tutorial to using Ptraj in generating DCCM
> (Daniel Roe)
> 23. Re: bad atom type: N3 (In MMGBSA decomp calculations)
> (Jason Swails)
> 24. amber2accent perl script (Manikanthan Bhavaraju)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 12 Jun 2013 11:01:21 -0700
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] ntt=2 on gpu
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <CDDE02B8.25BE5%ross.rosswalker.co.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> Hi Sarah,
>
> I believe that the jump in temperature seen at the beginning of the
> simulation with ntt=2 was coming from a missing CPU to GPU copy. I believe
> that it was purely cosmetic although don't have internet access right now
> to look back through the bug report but my recollection was that this was
> purely cosmetic in that it only effected the reported energies and not
> forces on which the trajectory is propagated.
>
> This arose because ntt=2 is rarely used with AMBER and so not extensively
> tested. My suggestion though would be to rerun the previous calculations
> if you can afford to. There are also some fixes for NPT they came out
> after the release of AMBER 12 so it certainly wouldn't help to rerun with
> the new code. At the very least rerun one of the previous simulations and
> see if you see any differences in your result analysis that can't be
> attributed to convergence difference in the sampling.
>
> All the best
> Ross
>
>
> On 6/10/13 11:34 AM, "Sarah Graham" <sarahgra.umich.edu> wrote:
>
> >Hi,
> >
> >We applied the newest bugfixes and it seems to be working fine now, thank
> >you. I had already run some simulations before I noticed these
> >temperature spikes. I was wondering what caused these temperature spikes
> >and do you think it would be necessary to redo all the previous
> >simulations
> >where this occurred? There seemed to be no problems in the resulting
> >trajectories that I can see, they look fine and all of the rmsd's are
> >fine.
> >Thanks for your help,
> >
> >Sarah Graham
> >
> >On Mon, Jun 10, 2013 at 10:12 AM, Ross Walker <ross.rosswalker.co.uk>
> >wrote:
> >
> >> Hi Sarah,
> >>
> >> Can you clarify whether you see this with AMBER 12 with the latest bug
> >> fixes please. That is your output file should contain the following:
> >>
> >> |--------------------- INFORMATION ----------------------
> >> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> >> | Version 12.3
> >> |
> >> | 04/24/2013
> >> |
> >>
> >>
> >>
> >> All the best
> >> Ross
> >>
> >>
> >>
> >> On 6/10/13 5:26 AM, "Sarah Graham" <sarahgra.umich.edu> wrote:
> >>
> >> >Sorry if this is a repeat, my emails don't seem to be going through.
> >> >
> >> >Hi,
> >> >
> >> >I have been running MD simulations on a gpu and am having issues when
> >> >restarting. I have ntt=2 and when restarting on gpu the first step
> >>has a
> >> >temperature of about 2000 instead of 300. I have irest=1 and ntx=5 so
> >> >velocity information should be read from the restart file. The restart
> >> >files are there and have information in them. When I run the same
> >> >simulations on cpu using the exact same input files the temperature
> >>does
> >> >not spike like this. Has anyone seen this before or know what might be
> >> >causing it? I am using Amber11 but I have also tried Amber12 and I
> >>still
> >> >have the same issue.
> >> >
> >> >Thanks for your help,
> >> >
> >> >Sarah Graham
> >> >
> >> >
> >> >input file
> >> >
> >> >Production run
> >> > &cntrl
> >> > imin = 0,
> >> > irest = 1, ntx = 5,
> >> > ntwe = 1000, ntwx = 1000, ntwr = 1000, ntpr = 1000, ntwv = 1000,
> >> > ntt = 2, temp0 = 300.0, tempi = 300.0,
> >> > dielc = 1, cut = 10.0,
> >> > ntb = 2, ntp = 1, ntc = 2, ntf = 2,
> >> > ig = -1,
> >> > nstlim = 1250000, dt = 0.0020,
> >> > /
> >> >
> >> >example output
> >> >
> >> >|-----------------------------
> >> >----------------------
> >> >Setting new random velocities at step 1000
> >> >check COM velocity, temp: 0.004194 0.03(Removed)
> >> >
> >> > NSTEP = 1000 TIME(PS) = 69332.000 TEMP(K) = 1860.02 PRESS =
> >> >-154.1
> >> > Etot = 28134.4824 EKtot = 174025.4076 EPtot =
> >> >-145890.9252
> >> > BOND = 696.4149 ANGLE = 1824.4578 DIHED =
> >> >2475.8020
> >> > 1-4 NB = 833.1366 1-4 EEL = 8244.7069 VDWAALS =
> >> >17977.2913
> >> > EELEC = -177942.7347 EHBOND = 0.0000 RESTRAINT =
> >> >0.0000
> >> > EKCMT = 12792.8104 VIRIAL = 14330.6250 VOLUME =
> >> >462044.0055
> >> > Density =
> >> >1.0133
> >> >
> >>
> >>>------------------------------------------------------------------------
> >>>--
> >> >----
> >> >
> >> >Setting new random velocities at step 2000
> >> >check COM velocity, temp: 0.000951 0.00(Removed)
> >> >
> >> > NSTEP = 2000 TIME(PS) = 69334.000 TEMP(K) = 300.63 PRESS =
> >> >-54.6
> >> > Etot = -117857.7631 EKtot = 28126.8179 EPtot =
> >> >-145984.5810
> >> > BOND = 734.8103 ANGLE = 1823.5534 DIHED =
> >> >2467.0220
> >> > 1-4 NB = 852.7348 1-4 EEL = 8202.9194 VDWAALS =
> >> >17875.8311
> >> > EELEC = -177941.4521 EHBOND = 0.0000 RESTRAINT =
> >> >0.0000
> >> >
> >> >203,2 1%
> >> >_______________________________________________
> >> >AMBER mailing list
> >> >AMBER.ambermd.org
> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 12 Jun 2013 16:56:58 -0400
> From: Hailin Huang <hailin.huang.my.liu.edu>
> Subject: [AMBER] Protein leaving periodic box
> To: amber.ambermd.org
> Message-ID:
> <CACOJS-44fOYqJLkpQYf3MQSGJzu-uFgxc5_U1OfhEtXCPQ9GRw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Amber users,
>
> I am running a prodution simulation of protein 3TNP in a 10A solvatebox.
> After about 25 ns of simlutation time, part of the protein drifts out of
> the solvent box. As the protein falls out further it breaks apart
> eventually and the fragment comes back in from the other side of the
> solvent box. Will I solve this problem by simply increasing the size of the
> solvent box? Is there a way to lock the protein within the box? Thanks for
> any help!
>
> The input file follows
>
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=2000, ntwx=2000, nstlim=2500000,
> dt=0.001, ntt=3, tempi=300,
> temp0=300, gamma_ln=1.0, ig=-1,
> ntp=0, ntc=2, ntf=2, cut=8,
> ntb=1, iwrap=1, ioutfm=1,
> /
>
> Regards,
> Richard
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 12 Jun 2013 15:07:58 -0600
> From: Benjamin Grant <bdgrant15.gmail.com>
> Subject: [AMBER] Running MD NPT Ensemble Error
> To: amber.ambermd.org
> Message-ID:
> <CAJYiP3Bvc-gY4a+Cf3TM9LoHKcOGnwSjbsj037jsV8oEBEraYg.mail.gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Hello,
>
> I?m modeling a carboxylic acid (palmitoleic and linoleic acids) and having
> issues with my MD simulations. I used the RESP methodology along with
> antechamber to get the necessary .prep and .frcmod files. I was able to
> successfully create a box (~25,000 atoms) for each carboxylic acid using
> packmol and tleap. I was also able successfully minimize the structure
> prior to starting my NPT simulations. The simulations seem to start out
> fine but they crash with the energy, temperature and the VDW contributions
> to the energy increasing. I also noticed that when ?wrapping first mol?
> appears for the first time in the md.out file, then my mdcrd and rst-crd
> file turn to ?****?. I have tried turning iwrap off and the problem still
> occurs. Also I?m unable to use VMD to see what is happening since the mdcrd
> file is filled with ?******?. I have attached my input and output files.
>
> I?m using Amber 12 with all of the bug fixes.
>
> Thanks,
>
> Ben
> -------------- next part --------------
>
> -------------------------------------------------------
> Amber 12 SANDER 2012
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 12
>
> | Run on 06/10/2013 at 09:46:27
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: md-npt.in
> | MDOUT: md.out
> | INPCRD: pta-rst.crd
> | PARM: pta.top
> | RESTRT: pta-rst-npt.crd
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> | MDINFO: mdinfo
>
>
> Here is the input file:
>
> nitial MD of cys
> &cntrl
> iwrap = 1,
> imin = 0,
> irest = 0,
> ntx = 1,
> nstlim = 5000000,
> dt = 0.002,
> ntwx = 1000,
> ntpr = 1000,
> ntb = 2,
> ntc = 2,
> ntf = 2,
> cut = 8,
> ntt = 3,
> ntp = 1,
> pres0 = 1,
> taup = 3,
> gamma_ln = 2.0,
> temp0 = 298.15,
> &end
>
>
>
>
>
>
>
>
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 12.2
> |
> | 01/10/2013
> |
> | Implementation by:
> | Ross C. Walker (SDSC)
> | Scott Le Grand (nVIDIA)
> | Duncan Poole (nVIDIA)
> |
> | CAUTION: The CUDA code is currently experimental.
> | You use it at your own risk. Be sure to
> | check ALL results carefully.
> |
> | Precision model in use:
> | [SPFP] - Mixed Single/Double/Fixed Point Precision.
> | (Default)
> |
> |--------------------------------------------------------
>
> |----------------- CITATION INFORMATION -----------------
> |
> | When publishing work that utilized the CUDA version
> | of AMBER, please cite the following in addition to
> | the regular AMBER citations:
> |
> | - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
> | Poole; Scott Le Grand; Ross C. Walker "Routine
> | microsecond molecular dynamics simulations with
> | AMBER - Part II: Particle Mesh Ewald", J. Chem.
> | Theory Comput., 2012, (In prep).
> |
> | - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
> | Duncan Poole; Scott Le Grand; Ross C. Walker
> | "Routine microsecond molecular dynamics simulations
> | with AMBER - Part I: Generalized Born", J. Chem.
> | Theory Comput., 2012, 8 (5), pp1542-1555.
> |
> | - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
> | "SPFP: Speed without compromise - a mixed precision
> | model for GPU accelerated molecular dynamics
> | simulations.", Comp. Phys. Comm., 2013, 184
> | pp374-380, DOI: 10.1016/j.cpc.2012.09.022
> |
> |--------------------------------------------------------
>
> |------------------- GPU DEVICE INFO --------------------
> |
> | CUDA Capable Devices Detected: 2
> | CUDA Device ID in use: 0
> | CUDA Device Name: GeForce GTX 680
> | CUDA Device Global Mem Size: 4095 MB
> | CUDA Device Num Multiprocessors: 8
> | CUDA Device Core Freq: 1.08 GHz
> |
> |--------------------------------------------------------
>
>
> | Conditional Compilation Defines Used:
> | DIRFRC_COMTRANS
> | DIRFRC_EFS
> | DIRFRC_NOVEC
> | PUBFFT
> | FFTLOADBAL_2PROC
> | BINTRAJ
> | CUDA
>
> | Largest sphere to fit in unit cell has radius = 45.000
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 06/08/13 Time = 18:06:39
>
> | Note: 1-4 EEL scale factors are being read from the topology file.
>
> | Note: 1-4 VDW scale factors are being read from the topology file.
> | Duplicated 0 dihedrals
>
> | Duplicated 0 dihedrals
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> getting new box info from bottom of inpcrd
>
> NATOM = 24000 NTYPES = 7 NBONH = 15000 MBONA = 8500
> NTHETH = 35500 MTHETA = 8500 NPHIH = 58500 MPHIA = 15500
> NHPARM = 0 NPARM = 0 NNB = 129500 NRES = 500
> NBONA = 8500 NTHETA = 8500 NPHIA = 15500 NUMBND = 9
> NUMANG = 14 NPTRA = 17 NATYP = 8 NPHB = 0
> IFBOX = 1 NMXRS = 48 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> | Coordinate Index Table dimensions: 19 19 19
> | Direct force subcell size = 4.7368 4.7368 4.7368
>
> BOX TYPE: RECTILINEAR
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
> --------------------------------------------------------------------------------
>
> default_name
>
> General flags:
> imin = 0, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 500
> iwrap = 1, ntwx = 1000, ntwv = 0, ntwe = 0
> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
>
> Potential function:
> ntf = 2, ntb = 2, igb = 0, nsnb = 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Molecular dynamics:
> nstlim = 5000000, nscm = 1000, nrespa = 1
> t = 0.00000, dt = 0.00200, vlimit = -1.00000
>
> Langevin dynamics temperature regulation:
> ig = 71277
> temp0 = 298.15000, tempi = 0.00000, gamma_ln= 2.00000
>
> Pressure regulation:
> ntp = 1
> pres0 = 1.00000, comp = 44.60000, taup = 3.00000
>
> SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00001
>
> | Intermolecular bonds treatment:
> | no_intermolecular_bonds = 1
>
> | Energy averages sample interval:
> | ene_avg_sampling = 1000
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 1
> Box X = 90.000 Box Y = 90.000 Box Z = 90.000
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 96 NFFT2 = 96 NFFT3 = 96
> Cutoff= 8.000 Tol =0.100E-04
> Ewald Coefficient = 0.34864
> Interpolation order = 4
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
> default_name
> begin time read from input coords = 0.000 ps
>
>
> Number of triangulated 3-point waters found: 0
>
> Sum of charges from parm topology file = -0.00149939
> Forcing neutrality...
>
> | Dynamic Memory, Types Used:
> | Reals 812294
> | Integers 2474574
>
> | Nonbonded Pairs Initial Allocation: 4008600
>
> | GPU memory information (estimate):
> | KB of GPU memory in use: 131143
> | KB of CPU memory in use: 48643
>
> --------------------------------------------------------------------------------
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> ---------------------------------------------------
> |---------------------------------------------------
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.47
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.89
> |---------------------------------------------------
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = -425.3
> Etot = -30776.0738 EKtot = 0.0000 EPtot = -30776.0738
> BOND = 298.9903 ANGLE = 1791.8943 DIHED = 9252.9745
> 1-4 NB = 2450.7868 1-4 EEL = -48243.3712 VDWAALS = -7791.6728
> EELEC = 11464.3244 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 0.0000 VIRIAL = 6693.5491 VOLUME = 729000.0000
> Density = 0.2897
> ------------------------------------------------------------------------------
>
>
> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 293.17 PRESS = -110.1
> Etot = 2010.2816 EKtot = 16603.4473 EPtot = -14593.1656
> BOND = 2943.8745 ANGLE = 12251.9097 DIHED = 11124.1786
> 1-4 NB = 3269.9698 1-4 EEL = -48569.6127 VDWAALS = -7144.6497
> EELEC = 11531.1642 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 446.2071 VIRIAL = 2170.7118 VOLUME = 725225.3117
> Density = 0.2913
> ------------------------------------------------------------------------------
>
>
> NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 297.96 PRESS = -168.3
> Etot = 1881.8804 EKtot = 16875.2070 EPtot = -14993.3266
> BOND = 3052.8955 ANGLE = 12254.6235 DIHED = 10854.3813
> 1-4 NB = 3309.1628 1-4 EEL = -48429.1372 VDWAALS = -7340.3221
> EELEC = 11305.0696 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 455.7567 VIRIAL = 3077.3308 VOLUME = 721471.9906
> Density = 0.2928
> ------------------------------------------------------------------------------
>
>
> NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 299.00 PRESS = -219.6
> Etot = 1684.1532 EKtot = 16933.6465 EPtot = -15249.4933
> BOND = 2987.0495 ANGLE = 12329.5468 DIHED = 10996.9982
> 1-4 NB = 3312.2000 1-4 EEL = -48321.1436 VDWAALS = -7536.8360
> EELEC = 10982.6919 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 459.4773 VIRIAL = 3862.8082 VOLUME = 717734.2760
> Density = 0.2943
> ------------------------------------------------------------------------------
>
>
> NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 296.84 PRESS = -155.9
> Etot = 1197.6240 EKtot = 16811.7754 EPtot = -15614.1514
> BOND = 3014.3511 ANGLE = 12243.7024 DIHED = 10995.5209
> 1-4 NB = 3322.7066 1-4 EEL = -48269.4342 VDWAALS = -7716.3541
> EELEC = 10795.3558 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 453.2439 VIRIAL = 2857.6158 VOLUME = 714336.2177
> Density = 0.2957
> ------------------------------------------------------------------------------
>
>
> NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 299.26 PRESS = -213.2
> Etot = 1028.3046 EKtot = 16948.6133 EPtot = -15920.3086
> BOND = 2989.4332 ANGLE = 12425.0543 DIHED = 10962.0963
> 1-4 NB = 3314.0339 1-4 EEL = -48463.2840 VDWAALS = -7954.7016
> EELEC = 10807.0592 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 448.8839 VIRIAL = 3721.4969 VOLUME = 710850.4553
> Density = 0.2971
> ------------------------------------------------------------------------------
>
>
> NSTEP = 6000 TIME(PS) = 12.000 TEMP(K) = 297.94 PRESS = -195.3
> Etot = 900.9802 EKtot = 16873.5723 EPtot = -15972.5921
> BOND = 2969.7081 ANGLE = 12359.9939 DIHED = 11066.1352
> 1-4 NB = 3280.0362 1-4 EEL = -48161.0580 VDWAALS = -8096.2043
> EELEC = 10608.7968 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 436.8430 VIRIAL = 3420.9351 VOLUME = 707819.1418
> Density = 0.2984
> ------------------------------------------------------------------------------
>
>
> NSTEP = 7000 TIME(PS) = 14.000 TEMP(K) = 299.72 PRESS = -127.4
> Etot = 653.2497 EKtot = 16974.6777 EPtot = -16321.4280
> BOND = 2929.4115 ANGLE = 12279.5385 DIHED = 10982.9334
> 1-4 NB = 3336.0082 1-4 EEL = -48174.1307 VDWAALS = -8169.7940
> EELEC = 10494.6050 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 467.4466 VIRIAL = 2406.6908 VOLUME = 705139.2963
> Density = 0.2995
> ------------------------------------------------------------------------------
>
>
> NSTEP = 8000 TIME(PS) = 16.000 TEMP(K) = 298.31 PRESS = -122.5
> Etot = 333.2306 EKtot = 16894.8594 EPtot = -16561.6288
> BOND = 2928.2379 ANGLE = 12304.3881 DIHED = 11039.2467
> 1-4 NB = 3332.0832 1-4 EEL = -48251.4847 VDWAALS = -8290.3134
> EELEC = 10376.2133 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 458.5630 VIRIAL = 2317.0753 VOLUME = 702845.3737
> Density = 0.3005
> ------------------------------------------------------------------------------
>
>
> NSTEP = 9000 TIME(PS) = 18.000 TEMP(K) = 298.89 PRESS = -52.4
> Etot = 253.6911 EKtot = 16927.7129 EPtot = -16674.0218
> BOND = 2921.7286 ANGLE = 12213.0462 DIHED = 10974.0835
> 1-4 NB = 3329.0859 1-4 EEL = -48197.3078 VDWAALS = -8244.3678
> EELEC = 10329.7097 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 468.2521 VIRIAL = 1260.4360 VOLUME = 700476.9416
> Density = 0.3015
> ------------------------------------------------------------------------------
>
>
> NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 299.74 PRESS = -78.2
> Etot = 273.8993 EKtot = 16976.0371 EPtot = -16702.1378
> BOND = 2924.3665 ANGLE = 12213.8043 DIHED = 11023.9935
> 1-4 NB = 3314.7666 1-4 EEL = -48049.0698 VDWAALS = -8304.6601
> EELEC = 10174.6613 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 447.8603 VIRIAL = 1626.6954 VOLUME = 698275.2518
> Density = 0.3025
> ------------------------------------------------------------------------------
>
>
> NSTEP = 11000 TIME(PS) = 22.000 TEMP(K) = 297.17 PRESS = -89.6
> Etot = 53.8154 EKtot = 16830.2188 EPtot = -16776.4033
> BOND = 2982.3938 ANGLE = 12165.4244 DIHED = 11033.9518
> 1-4 NB = 3315.6680 1-4 EEL = -48097.1446 VDWAALS = -8305.8624
> EELEC = 10129.1657 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 446.1796 VIRIAL = 1792.9852 VOLUME = 695893.1082
> Density = 0.3035
> ------------------------------------------------------------------------------
>
>
> NSTEP = 12000 TIME(PS) = 24.000 TEMP(K) = 298.78 PRESS = -161.1
> Etot = 60.4924 EKtot = 16921.5723 EPtot = -16861.0799
> BOND = 2885.7054 ANGLE = 12282.9697 DIHED = 11098.6696
> 1-4 NB = 3347.8918 1-4 EEL = -48091.8621 VDWAALS = -8456.7509
> EELEC = 10072.2967 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 438.4510 VIRIAL = 2850.3812 VOLUME = 693335.5729
> Density = 0.3046
> ------------------------------------------------------------------------------
>
>
> NSTEP = 13000 TIME(PS) = 26.000 TEMP(K) = 298.35 PRESS = -67.7
> Etot = -60.8389 EKtot = 16896.8242 EPtot = -16957.6632
> BOND = 2936.6219 ANGLE = 12195.9215 DIHED = 11107.5915
> 1-4 NB = 3294.7467 1-4 EEL = -48090.0334 VDWAALS = -8313.7707
> EELEC = 9911.2592 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 448.0089 VIRIAL = 1458.4201 VOLUME = 691135.8622
> Density = 0.3056
> ------------------------------------------------------------------------------
>
>
> NSTEP = 14000 TIME(PS) = 28.000 TEMP(K) = 301.90 PRESS = -129.7
> Etot = 9.1456 EKtot = 17098.1055 EPtot = -17088.9599
> BOND = 3014.9112 ANGLE = 12118.8379 DIHED = 11081.5387
> 1-4 NB = 3323.3371 1-4 EEL = -48085.9205 VDWAALS = -8485.6222
> EELEC = 9943.9579 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 431.0440 VIRIAL = 2359.1745 VOLUME = 688666.1569
> Density = 0.3067
> ------------------------------------------------------------------------------
>
>
> NSTEP = 15000 TIME(PS) = 30.000 TEMP(K) = 299.77 PRESS = -77.0
> Etot = -132.1634 EKtot = 16977.1895 EPtot = -17109.3528
> BOND = 2967.7553 ANGLE = 12102.7041 DIHED = 11137.3671
> 1-4 NB = 3348.7899 1-4 EEL = -48004.2595 VDWAALS = -8564.9638
> EELEC = 9903.2542 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 469.4089 VIRIAL = 1610.5678 VOLUME = 686069.8453
> Density = 0.3079
> ------------------------------------------------------------------------------
>
>
> NSTEP = 16000 TIME(PS) = 32.000 TEMP(K) = 297.96 PRESS = -97.6
> Etot = -469.5359 EKtot = 16874.8750 EPtot = -17344.4109
> BOND = 2965.6459 ANGLE = 12140.1513 DIHED = 11050.7943
> 1-4 NB = 3314.2238 1-4 EEL = -48038.9540 VDWAALS = -8652.2362
> EELEC = 9875.9640 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 426.9781 VIRIAL = 1868.3659 VOLUME = 683737.6987
> Density = 0.3089
> ------------------------------------------------------------------------------
>
>
> NSTEP = 17000 TIME(PS) = 34.000 TEMP(K) = 299.92 PRESS = -112.9
> Etot = -290.1739 EKtot = 16985.9473 EPtot = -17276.1212
> BOND = 2955.4954 ANGLE = 12081.3039 DIHED = 11114.6340
> 1-4 NB = 3287.8886 1-4 EEL = -47936.5659 VDWAALS = -8566.2027
> EELEC = 9787.3255 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 420.5328 VIRIAL = 2081.4516 VOLUME = 681361.1964
> Density = 0.3100
> ------------------------------------------------------------------------------
>
>
> NSTEP = 18000 TIME(PS) = 36.000 TEMP(K) = 296.64 PRESS = -167.6
> Etot = -581.9320 EKtot = 16800.3691 EPtot = -17382.3011
> BOND = 2903.1138 ANGLE = 12096.5638 DIHED = 11110.8781
> 1-4 NB = 3314.9914 1-4 EEL = -48054.2910 VDWAALS = -8606.2334
> EELEC = 9852.6763 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 452.0211 VIRIAL = 2909.0044 VOLUME = 678983.6899
> Density = 0.3111
> ------------------------------------------------------------------------------
>
>
> NSTEP = 19000 TIME(PS) = 38.000 TEMP(K) = 296.41 PRESS = -124.4
> Etot = -503.2364 EKtot = 16787.3867 EPtot = -17290.6232
> BOND = 2949.2154 ANGLE = 12164.5565 DIHED = 11148.1759
> 1-4 NB = 3285.0978 1-4 EEL = -47954.4186 VDWAALS = -8634.4695
> EELEC = 9751.2193 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 471.6721 VIRIAL = 2288.0730 VOLUME = 676430.7196
> Density = 0.3123
> ------------------------------------------------------------------------------
>
>
> NSTEP = 20000 TIME(PS) = 40.000 TEMP(K) = 300.52 PRESS = -79.1
> Etot = -367.5910 EKtot = 17020.0781 EPtot = -17387.6691
> BOND = 2931.9721 ANGLE = 12223.8421 DIHED = 11083.1000
> 1-4 NB = 3274.6981 1-4 EEL = -47880.6111 VDWAALS = -8646.0262
> EELEC = 9625.3559 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 434.8684 VIRIAL = 1586.6701 VOLUME = 674222.4417
> Density = 0.3133
> ------------------------------------------------------------------------------
>
>
> NSTEP = 21000 TIME(PS) = 42.000 TEMP(K) = 297.22 PRESS = -152.5
> Etot = -656.2506 EKtot = 16832.9707 EPtot = -17489.2213
> BOND = 2934.0730 ANGLE = 12104.5918 DIHED = 11138.2089
> 1-4 NB = 3288.3346 1-4 EEL = -47887.3828 VDWAALS = -8752.4890
> EELEC = 9685.4421 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 443.6293 VIRIAL = 2656.6810 VOLUME = 672048.6170
> Density = 0.3143
> ------------------------------------------------------------------------------
>
>
> NSTEP = 22000 TIME(PS) = 44.000 TEMP(K) = 296.63 PRESS = -54.7
> Etot = -701.8416 EKtot = 16799.3496 EPtot = -17501.1912
> BOND = 2918.6450 ANGLE = 12137.9241 DIHED = 11149.2967
> 1-4 NB = 3305.4339 1-4 EEL = -47903.8288 VDWAALS = -8705.7979
> EELEC = 9597.1358 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 467.0359 VIRIAL = 1258.1859 VOLUME = 669947.2575
> Density = 0.3153
> ------------------------------------------------------------------------------
>
>
> NSTEP = 23000 TIME(PS) = 46.000 TEMP(K) = 299.50 PRESS = -75.7
> Etot = -546.4606 EKtot = 16962.3223 EPtot = -17508.7829
> BOND = 3017.1226 ANGLE = 12148.3401 DIHED = 11125.8749
> 1-4 NB = 3253.1107 1-4 EEL = -47943.9242 VDWAALS = -8610.4654
> EELEC = 9501.1584 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 446.2237 VIRIAL = 1538.5842 VOLUME = 668296.3414
> Density = 0.3161
> ------------------------------------------------------------------------------
>
>
> NSTEP = 24000 TIME(PS) = 48.000 TEMP(K) = 297.53 PRESS = -121.5
> Etot = -619.7796 EKtot = 16850.8027 EPtot = -17470.5823
> BOND = 2997.9306 ANGLE = 12197.0746 DIHED = 11091.0137
> 1-4 NB = 3272.4955 1-4 EEL = -47854.8766 VDWAALS = -8668.9636
> EELEC = 9494.7435 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 423.1948 VIRIAL = 2169.1779 VOLUME = 665768.5649
> Density = 0.3173
> ------------------------------------------------------------------------------
>
>
> NSTEP = 25000 TIME(PS) = 50.000 TEMP(K) = 300.89 PRESS = -180.5
> Etot = -410.4481 EKtot = 17041.1445 EPtot = -17451.5927
> BOND = 2950.2251 ANGLE = 12224.8813 DIHED = 11157.0662
> 1-4 NB = 3330.2234 1-4 EEL = -47908.7988 VDWAALS = -8717.6692
> EELEC = 9512.4793 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 428.3658 VIRIAL = 3013.0189 VOLUME = 663102.1398
> Density = 0.3185
> ------------------------------------------------------------------------------
>
>
> NSTEP = 26000 TIME(PS) = 52.000 TEMP(K) = 296.74 PRESS = -91.2
> Etot = -813.7549 EKtot = 16805.9512 EPtot = -17619.7061
> BOND = 2959.0650 ANGLE = 12120.2389 DIHED = 11086.1549
> 1-4 NB = 3315.9108 1-4 EEL = -47882.5186 VDWAALS = -8719.0262
> EELEC = 9500.4690 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 446.5824 VIRIAL = 1747.7227 VOLUME = 660675.9271
> Density = 0.3197
> ------------------------------------------------------------------------------
>
>
> NSTEP = 27000 TIME(PS) = 54.000 TEMP(K) = 299.67 PRESS = -93.5
> Etot = -586.1301 EKtot = 16971.9414 EPtot = -17558.0715
> BOND = 2954.0225 ANGLE = 12173.3919 DIHED = 11195.5900
> 1-4 NB = 3297.8960 1-4 EEL = -47882.9659 VDWAALS = -8765.3082
> EELEC = 9469.3023 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 435.2850 VIRIAL = 1765.2108 VOLUME = 658684.7833
> Density = 0.3207
> ------------------------------------------------------------------------------
>
>
> NSTEP = 28000 TIME(PS) = 56.000 TEMP(K) = 298.79 PRESS = -83.1
> Etot = -565.0315 EKtot = 16921.8770 EPtot = -17486.9085
> BOND = 2967.8736 ANGLE = 12180.8108 DIHED = 11133.9560
> 1-4 NB = 3294.2167 1-4 EEL = -47737.5232 VDWAALS = -8722.7036
> EELEC = 9396.4611 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 468.2442 VIRIAL = 1645.6294 VOLUME = 656214.7816
> Density = 0.3219
> ------------------------------------------------------------------------------
>
>
> NSTEP = 29000 TIME(PS) = 58.000 TEMP(K) = 299.40 PRESS = -160.5
> Etot = -896.5703 EKtot = 16956.5469 EPtot = -17853.1171
> BOND = 2951.0301 ANGLE = 12110.8001 DIHED = 11090.7794
> 1-4 NB = 3265.1846 1-4 EEL = -47817.0578 VDWAALS = -8828.0242
> EELEC = 9374.1707 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 431.8764 VIRIAL = 2699.6432 VOLUME = 654245.7294
> Density = 0.3229
> ------------------------------------------------------------------------------
>
>
> NSTEP = 30000 TIME(PS) = 60.000 TEMP(K) = 298.90 PRESS = -41.7
> Etot = -799.0401 EKtot = 16928.0566 EPtot = -17727.0968
> BOND = 2971.5284 ANGLE = 12281.0224 DIHED = 11195.7654
> 1-4 NB = 3264.1643 1-4 EEL = -47947.0888 VDWAALS = -8852.9019
> EELEC = 9360.4135 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 423.8819 VIRIAL = 1011.0635 VOLUME = 651865.6955
> Density = 0.3240
> ------------------------------------------------------------------------------
>
>
> NSTEP = 31000 TIME(PS) = 62.000 TEMP(K) = 298.91 PRESS = -19.0
> Etot = -836.6389 EKtot = 16928.9980 EPtot = -17765.6370
> BOND = 2998.7419 ANGLE = 12146.8690 DIHED = 11184.0935
> 1-4 NB = 3269.2858 1-4 EEL = -47819.3213 VDWAALS = -8847.4619
> EELEC = 9302.1560 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 431.2818 VIRIAL = 697.7076 VOLUME = 649750.3077
> Density = 0.3251
> ------------------------------------------------------------------------------
>
>
> NSTEP = 32000 TIME(PS) = 64.000 TEMP(K) = 298.40 PRESS = -119.5
> Etot = -1052.1937 EKtot = 16900.0859 EPtot = -17952.2796
> BOND = 2973.8668 ANGLE = 12062.4696 DIHED = 11138.4063
> 1-4 NB = 3270.0160 1-4 EEL = -47847.6668 VDWAALS = -8913.8746
> EELEC = 9364.5030 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 454.0004 VIRIAL = 2125.2075 VOLUME = 647795.9425
> Density = 0.3261
> ------------------------------------------------------------------------------
>
>
> NSTEP = 33000 TIME(PS) = 66.000 TEMP(K) = 298.03 PRESS = -82.4
> Etot = -966.4535 EKtot = 16879.1035 EPtot = -17845.5571
> BOND = 2964.8414 ANGLE = 12164.6272 DIHED = 11183.0349
> 1-4 NB = 3271.5584 1-4 EEL = -47820.8866 VDWAALS = -8886.6003
> EELEC = 9277.8679 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 412.5457 VIRIAL = 1561.0761 VOLUME = 645498.4076
> Density = 0.3272
> ------------------------------------------------------------------------------
>
>
> NSTEP = 34000 TIME(PS) = 68.000 TEMP(K) = 296.33 PRESS = -187.5
> Etot = -963.3059 EKtot = 16782.6465 EPtot = -17745.9524
> BOND = 2982.2380 ANGLE = 12323.1562 DIHED = 11135.8765
> 1-4 NB = 3301.8871 1-4 EEL = -47903.7317 VDWAALS = -8903.9533
> EELEC = 9318.5748 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 455.3157 VIRIAL = 3059.9749 VOLUME = 643509.2852
> Density = 0.3282
> ------------------------------------------------------------------------------
>
>
> NSTEP = 35000 TIME(PS) = 70.000 TEMP(K) = 299.23 PRESS = -88.9
> Etot = -966.9638 EKtot = 16946.8242 EPtot = -17913.7880
> BOND = 2923.5464 ANGLE = 12169.4289 DIHED = 11147.7043
> 1-4 NB = 3257.3959 1-4 EEL = -47780.2464 VDWAALS = -8817.8007
> EELEC = 9186.1836 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 443.6985 VIRIAL = 1674.9567 VOLUME = 641735.8726
> Density = 0.3291
> ------------------------------------------------------------------------------
>
>
> NSTEP = 36000 TIME(PS) = 72.000 TEMP(K) = 297.33 PRESS = -80.7
> Etot = -1057.2085 EKtot = 16839.2207 EPtot = -17896.4292
> BOND = 2954.3267 ANGLE = 12175.7894 DIHED = 11129.9138
> 1-4 NB = 3260.5883 1-4 EEL = -47787.5094 VDWAALS = -8881.6898
> EELEC = 9252.1518 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 431.3623 VIRIAL = 1545.3955 VOLUME = 639544.0058
> Density = 0.3303
> ------------------------------------------------------------------------------
>
>
> NSTEP = 37000 TIME(PS) = 74.000 TEMP(K) = 296.39 PRESS = -87.9
> Etot = -1184.7701 EKtot = 16786.0879 EPtot = -17970.8580
> BOND = 2975.7500 ANGLE = 12043.1416 DIHED = 11105.8529
> 1-4 NB = 3328.8042 1-4 EEL = -47825.0526 VDWAALS = -8809.2589
> EELEC = 9209.9048 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 450.9133 VIRIAL = 1661.0903 VOLUME = 637896.4104
> Density = 0.3311
> ------------------------------------------------------------------------------
>
>
> NSTEP = 38000 TIME(PS) = 76.000 TEMP(K) = 297.55 PRESS = -107.0
> Etot = -947.6454 EKtot = 16851.4961 EPtot = -17799.1415
> BOND = 2993.4416 ANGLE = 12103.4474 DIHED = 11156.6967
> 1-4 NB = 3262.9428 1-4 EEL = -47645.8908 VDWAALS = -8794.0370
> EELEC = 9124.2579 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 465.2583 VIRIAL = 1934.0021 VOLUME = 635547.5374
> Density = 0.3323
> ------------------------------------------------------------------------------
>
>
> NSTEP = 39000 TIME(PS) = 78.000 TEMP(K) = 299.66 PRESS = -150.8
> Etot = -1200.2538 EKtot = 16971.3965 EPtot = -18171.6503
> BOND = 2955.5535 ANGLE = 12059.3232 DIHED = 11080.4591
> 1-4 NB = 3257.2390 1-4 EEL = -47792.0270 VDWAALS = -8886.0637
> EELEC = 9153.8657 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 425.1916 VIRIAL = 2488.2998 VOLUME = 633637.6032
> Density = 0.3334
> ------------------------------------------------------------------------------
>
>
> NSTEP = 40000 TIME(PS) = 80.000 TEMP(K) = 298.06 PRESS = -107.6
> Etot = -1110.1149 EKtot = 16880.6504 EPtot = -17990.7652
> BOND = 2869.5330 ANGLE = 12129.4178 DIHED = 11124.3354
> 1-4 NB = 3269.8472 1-4 EEL = -47709.7388 VDWAALS = -8821.7260
> EELEC = 9147.5662 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 461.9418 VIRIAL = 1929.5720 VOLUME = 631611.1958
> Density = 0.3344
> ------------------------------------------------------------------------------
>
>
> NSTEP = 41000 TIME(PS) = 82.000 TEMP(K) = 297.33 PRESS = -154.5
> Etot = -1231.0233 EKtot = 16839.5508 EPtot = -18070.5741
> BOND = 2951.5070 ANGLE = 11931.5478 DIHED = 11162.5615
> 1-4 NB = 3265.1675 1-4 EEL = -47625.7380 VDWAALS = -8914.1150
> EELEC = 9158.4950 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 451.3626 VIRIAL = 2552.1103 VOLUME = 629785.2042
> Density = 0.3354
> ------------------------------------------------------------------------------
>
>
> NSTEP = 42000 TIME(PS) = 84.000 TEMP(K) = 298.67 PRESS = -77.6
> Etot = -992.4574 EKtot = 16915.3242 EPtot = -17907.7816
> BOND = 2962.9744 ANGLE = 12039.7747 DIHED = 11255.6934
> 1-4 NB = 3280.3554 1-4 EEL = -47808.4373 VDWAALS = -8807.6756
> EELEC = 9169.5334 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 425.5595 VIRIAL = 1477.7604 VOLUME = 627965.5390
> Density = 0.3364
> ------------------------------------------------------------------------------
>
>
> NSTEP = 43000 TIME(PS) = 86.000 TEMP(K) = 298.01 PRESS = -116.1
> Etot = -926.8599 EKtot = 16877.9551 EPtot = -17804.8149
> BOND = 3011.6045 ANGLE = 12188.3911 DIHED = 11217.8093
> 1-4 NB = 3293.4306 1-4 EEL = -47761.1641 VDWAALS = -8865.8269
> EELEC = 9110.9406 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 430.6443 VIRIAL = 1999.7264 VOLUME = 625717.7853
> Density = 0.3376
> ------------------------------------------------------------------------------
>
>
> NSTEP = 44000 TIME(PS) = 88.000 TEMP(K) = 295.24 PRESS = -172.9
> Etot = -1339.1050 EKtot = 16721.1816 EPtot = -18060.2866
> BOND = 2924.6385 ANGLE = 12121.7719 DIHED = 11189.4374
> 1-4 NB = 3289.4858 1-4 EEL = -47841.3499 VDWAALS = -8835.2854
> EELEC = 9091.0152 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 425.5802 VIRIAL = 2752.7658 VOLUME = 623339.9080
> Density = 0.3389
> ------------------------------------------------------------------------------
>
>
> NSTEP = 45000 TIME(PS) = 90.000 TEMP(K) = 296.39 PRESS = -73.4
> Etot = -1153.4194 EKtot = 16785.9883 EPtot = -17939.4077
> BOND = 2978.3627 ANGLE = 12063.6167 DIHED = 11233.2513
> 1-4 NB = 3305.7973 1-4 EEL = -47795.5967 VDWAALS = -8833.3383
> EELEC = 9108.4991 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 417.8091 VIRIAL = 1402.0154 VOLUME = 621163.5114
> Density = 0.3400
> ------------------------------------------------------------------------------
>
>
> NSTEP = 46000 TIME(PS) = 92.000 TEMP(K) = 298.69 PRESS = -0.7
> Etot = -1145.5509 EKtot = 16916.4277 EPtot = -18061.9787
> BOND = 2888.7372 ANGLE = 12095.7241 DIHED = 11104.0575
> 1-4 NB = 3287.6815 1-4 EEL = -47716.0509 VDWAALS = -8804.5227
> EELEC = 9082.3946 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 459.0961 VIRIAL = 468.1078 VOLUME = 618970.7345
> Density = 0.3413
> ------------------------------------------------------------------------------
>
>
> NSTEP = 47000 TIME(PS) = 94.000 TEMP(K) = 299.82 PRESS = -129.9
> Etot = -1007.6778 EKtot = 16980.4980 EPtot = -17988.1758
> BOND = 2954.0737 ANGLE = 12131.3710 DIHED = 11190.6544
> 1-4 NB = 3318.7403 1-4 EEL = -47820.2608 VDWAALS = -8894.7952
> EELEC = 9132.0406 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 502.9602 VIRIAL = 2234.3258 VOLUME = 617273.4166
> Density = 0.3422
> ------------------------------------------------------------------------------
>
>
> NSTEP = 48000 TIME(PS) = 96.000 TEMP(K) = 298.16 PRESS = -84.5
> Etot = -1043.0086 EKtot = 16886.0664 EPtot = -17929.0750
> BOND = 2883.1201 ANGLE = 12238.3759 DIHED = 11175.5378
> 1-4 NB = 3288.9057 1-4 EEL = -47768.0564 VDWAALS = -8822.5513
> EELEC = 9075.5932 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 433.7954 VIRIAL = 1556.0810 VOLUME = 615444.5233
> Density = 0.3432
> ------------------------------------------------------------------------------
>
>
> NSTEP = 49000 TIME(PS) = 98.000 TEMP(K) = 301.36 PRESS = -186.5
> Etot = -849.4635 EKtot = 17067.7461 EPtot = -17917.2096
> BOND = 3009.1174 ANGLE = 12105.2409 DIHED = 11191.9429
> 1-4 NB = 3316.8750 1-4 EEL = -47765.7937 VDWAALS = -8888.3466
> EELEC = 9113.7546 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 431.5593 VIRIAL = 2901.4180 VOLUME = 613226.0957
> Density = 0.3444
> ------------------------------------------------------------------------------
>
>
> NSTEP = 50000 TIME(PS) = 100.000 TEMP(K) = 299.39 PRESS = -74.0
> Etot = -1261.3287 EKtot = 16955.7910 EPtot = -18217.1197
> BOND = 2968.5775 ANGLE = 12019.4127 DIHED = 11198.5906
> 1-4 NB = 3247.3066 1-4 EEL = -47675.8836 VDWAALS = -8952.7411
> EELEC = 8977.6177 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 453.9316 VIRIAL = 1431.6182 VOLUME = 611645.8098
> Density = 0.3453
> ------------------------------------------------------------------------------
>
>
> NSTEP = 51000 TIME(PS) = 102.000 TEMP(K) = 298.91 PRESS = -71.2
> Etot = -1043.3526 EKtot = 16928.5371 EPtot = -17971.8897
> BOND = 2898.8556 ANGLE = 12220.4217 DIHED = 11127.8360
> 1-4 NB = 3298.0783 1-4 EEL = -47672.6760 VDWAALS = -8839.1780
> EELEC = 8994.7727 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 433.3300 VIRIAL = 1371.6001 VOLUME = 609949.4782
> Density = 0.3463
> ------------------------------------------------------------------------------
>
>
> NSTEP = 52000 TIME(PS) = 104.000 TEMP(K) = 299.58 PRESS = -139.7
> Etot = -1189.4586 EKtot = 16966.5547 EPtot = -18156.0133
> BOND = 3007.5791 ANGLE = 12177.1376 DIHED = 11055.3905
> 1-4 NB = 3249.6795 1-4 EEL = -47785.1230 VDWAALS = -8993.3579
> EELEC = 9132.6811 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 462.4717 VIRIAL = 2297.6168 VOLUME = 608196.9859
> Density = 0.3473
> ------------------------------------------------------------------------------
>
>
> NSTEP = 53000 TIME(PS) = 106.000 TEMP(K) = 300.17 PRESS = -4.9
> Etot = -1260.2963 EKtot = 17000.3613 EPtot = -18260.6576
> BOND = 2985.3902 ANGLE = 12047.1217 DIHED = 11075.6463
> 1-4 NB = 3265.7706 1-4 EEL = -47757.0371 VDWAALS = -8949.7547
> EELEC = 9072.2053 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 474.2066 VIRIAL = 537.7252 VOLUME = 606496.1737
> Density = 0.3483
> ------------------------------------------------------------------------------
>
>
> NSTEP = 54000 TIME(PS) = 108.000 TEMP(K) = 297.13 PRESS = -56.4
> Etot = -1299.2460 EKtot = 16828.0586 EPtot = -18127.3046
> BOND = 2929.4365 ANGLE = 12057.3349 DIHED = 11191.6986
> 1-4 NB = 3295.4382 1-4 EEL = -47617.2747 VDWAALS = -8946.9710
> EELEC = 8963.0330 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 423.4167 VIRIAL = 1159.4094 VOLUME = 604716.3445
> Density = 0.3493
> ------------------------------------------------------------------------------
>
>
> NSTEP = 55000 TIME(PS) = 110.000 TEMP(K) = 295.01 PRESS = -93.2
> Etot = -1525.9908 EKtot = 16707.8145 EPtot = -18233.8052
> BOND = 2949.2998 ANGLE = 12013.1803 DIHED = 11133.3775
> 1-4 NB = 3304.2636 1-4 EEL = -47671.7366 VDWAALS = -8916.1060
> EELEC = 8953.9162 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 466.1491 VIRIAL = 1679.7802 VOLUME = 603063.1738
> Density = 0.3503
> ------------------------------------------------------------------------------
>
>
> NSTEP = 56000 TIME(PS) = 112.000 TEMP(K) = 298.58 PRESS = -142.7
> Etot = -1315.2436 EKtot = 16910.2520 EPtot = -18225.4956
> BOND = 2875.8006 ANGLE = 12061.9930 DIHED = 11186.4270
> 1-4 NB = 3302.2252 1-4 EEL = -47687.0881 VDWAALS = -8949.9058
> EELEC = 8985.0526 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 439.9691 VIRIAL = 2292.2503 VOLUME = 601098.1568
> Density = 0.3514
> ------------------------------------------------------------------------------
>
>
> NSTEP = 57000 TIME(PS) = 114.000 TEMP(K) = 297.15 PRESS = -53.7
> Etot = -1282.1595 EKtot = 16829.0586 EPtot = -18111.2181
> BOND = 2923.1194 ANGLE = 12221.5493 DIHED = 11140.8094
> 1-4 NB = 3282.6900 1-4 EEL = -47715.2963 VDWAALS = -8858.8714
> EELEC = 8894.7814 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 430.3507 VIRIAL = 1125.2845 VOLUME = 599548.5045
> Density = 0.3523
> ------------------------------------------------------------------------------
>
>
> NSTEP = 58000 TIME(PS) = 116.000 TEMP(K) = 297.99 PRESS = -230.4
> Etot = -1251.4593 EKtot = 16876.9082 EPtot = -18128.3676
> BOND = 2997.5867 ANGLE = 11938.6757 DIHED = 11261.7796
> 1-4 NB = 3278.7537 1-4 EEL = -47534.0552 VDWAALS = -8984.0145
> EELEC = 8912.9064 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 445.2146 VIRIAL = 3420.8669 VOLUME = 598293.1366
> Density = 0.3530
> ------------------------------------------------------------------------------
>
>
> NSTEP = 59000 TIME(PS) = 118.000 TEMP(K) = 300.27 PRESS = -93.1
> Etot = -1204.4745 EKtot = 17005.6465 EPtot = -18210.1210
> BOND = 2995.7976 ANGLE = 12003.9547 DIHED = 11121.8067
> 1-4 NB = 3281.1473 1-4 EEL = -47701.8153 VDWAALS = -8854.9946
> EELEC = 8943.9826 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 482.6051 VIRIAL = 1681.0851 VOLUME = 596111.1207
> Density = 0.3543
> ------------------------------------------------------------------------------
>
>
> NSTEP = 60000 TIME(PS) = 120.000 TEMP(K) = 299.42 PRESS = -157.9
> Etot = -1258.5839 EKtot = 16957.8574 EPtot = -18216.4414
> BOND = 2969.9594 ANGLE = 12045.1076 DIHED = 11184.4262
> 1-4 NB = 3258.5184 1-4 EEL = -47629.4893 VDWAALS = -8989.7082
> EELEC = 8944.7446 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 455.1968 VIRIAL = 2481.4351 VOLUME = 594482.3995
> Density = 0.3553
> ------------------------------------------------------------------------------
>
>
> NSTEP = 61000 TIME(PS) = 122.000 TEMP(K) = 298.57 PRESS = -136.1
> Etot = -1314.5424 EKtot = 16909.6719 EPtot = -18224.2143
> BOND = 2978.3790 ANGLE = 12080.4928 DIHED = 11122.0401
> 1-4 NB = 3229.3014 1-4 EEL = -47749.8634 VDWAALS = -8904.0457
> EELEC = 9019.4815 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 429.9368 VIRIAL = 2171.5182 VOLUME = 592724.2839
> Density = 0.3564
> ------------------------------------------------------------------------------
>
>
> NSTEP = 62000 TIME(PS) = 124.000 TEMP(K) = 300.58 PRESS = -53.4
> Etot = -1226.0613 EKtot = 17023.3262 EPtot = -18249.3875
> BOND = 2967.9347 ANGLE = 11941.7893 DIHED = 11159.1195
> 1-4 NB = 3287.6104 1-4 EEL = -47717.1669 VDWAALS = -8833.2657
> EELEC = 8944.5912 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 461.4962 VIRIAL = 1142.5568 VOLUME = 590832.9968
> Density = 0.3575
> ------------------------------------------------------------------------------
>
>
> NSTEP = 63000 TIME(PS) = 126.000 TEMP(K) = 298.21 PRESS = -135.2
> Etot = -1377.8465 EKtot = 16889.1152 EPtot = -18266.9617
> BOND = 2967.1645 ANGLE = 11998.1041 DIHED = 11162.3164
> 1-4 NB = 3269.7751 1-4 EEL = -47787.9885 VDWAALS = -8885.0889
> EELEC = 9008.7556 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 451.4819 VIRIAL = 2169.9375 VOLUME = 588901.8197
> Density = 0.3587
> ------------------------------------------------------------------------------
>
>
> NSTEP = 64000 TIME(PS) = 128.000 TEMP(K) = 298.92 PRESS = -99.8
> Etot = -1218.5543 EKtot = 16929.1973 EPtot = -18147.7515
> BOND = 2992.0261 ANGLE = 12016.2395 DIHED = 11152.9793
> 1-4 NB = 3271.0161 1-4 EEL = -47647.4492 VDWAALS = -8916.8483
> EELEC = 8984.2848 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 457.0370 VIRIAL = 1721.3533 VOLUME = 586916.6769
> Density = 0.3599
> ------------------------------------------------------------------------------
>
>
> NSTEP = 65000 TIME(PS) = 130.000 TEMP(K) = 292.16 PRESS = -174.1
> Etot = -1803.6625 EKtot = 16546.7324 EPtot = -18350.3949
> BOND = 2896.8980 ANGLE = 12019.6219 DIHED = 11161.7558
> 1-4 NB = 3299.0080 1-4 EEL = -47742.0477 VDWAALS = -8886.3447
> EELEC = 8900.7138 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 444.3993 VIRIAL = 2641.1623 VOLUME = 584498.8570
> Density = 0.3614
> ------------------------------------------------------------------------------
>
>
> NSTEP = 66000 TIME(PS) = 132.000 TEMP(K) = 295.69 PRESS = -70.9
> Etot = -1340.2815 EKtot = 16746.5371 EPtot = -18086.8186
> BOND = 2930.8510 ANGLE = 12101.9061 DIHED = 11202.2186
> 1-4 NB = 3299.5063 1-4 EEL = -47654.2586 VDWAALS = -8849.4231
> EELEC = 8882.3810 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 460.4249 VIRIAL = 1351.4435 VOLUME = 582276.0308
> Density = 0.3628
> ------------------------------------------------------------------------------
>
>
> NSTEP = 67000 TIME(PS) = 134.000 TEMP(K) = 298.02 PRESS = -96.6
> Etot = -1339.6056 EKtot = 16878.2773 EPtot = -18217.8829
> BOND = 2903.9358 ANGLE = 12143.7031 DIHED = 11168.6807
> 1-4 NB = 3257.3555 1-4 EEL = -47731.1837 VDWAALS = -8880.5401
> EELEC = 8920.1658 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 430.1543 VIRIAL = 1639.2987 VOLUME = 579823.4155
> Density = 0.3643
> ------------------------------------------------------------------------------
>
>
> NSTEP = 68000 TIME(PS) = 136.000 TEMP(K) = 296.27 PRESS = -118.8
> Etot = -1371.2336 EKtot = 16779.0332 EPtot = -18150.2668
> BOND = 2909.9803 ANGLE = 12196.4041 DIHED = 11172.6713
> 1-4 NB = 3285.5001 1-4 EEL = -47733.2418 VDWAALS = -8883.5528
> EELEC = 8901.9719 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 450.3974 VIRIAL = 1932.4875 VOLUME = 577589.1731
> Density = 0.3657
> ------------------------------------------------------------------------------
>
>
> NSTEP = 69000 TIME(PS) = 138.000 TEMP(K) = 298.44 PRESS = -220.0
> Etot = -1376.5554 EKtot = 16902.3184 EPtot = -18278.8738
> BOND = 2935.8731 ANGLE = 12061.9525 DIHED = 11222.8676
> 1-4 NB = 3263.3560 1-4 EEL = -47680.4601 VDWAALS = -8956.1978
> EELEC = 8873.7350 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 450.3924 VIRIAL = 3182.8558 VOLUME = 575361.3296
> Density = 0.3671
> ------------------------------------------------------------------------------
>
>
> NSTEP = 70000 TIME(PS) = 140.000 TEMP(K) = 298.64 PRESS = -115.0
> Etot = -1267.9109 EKtot = 16913.1836 EPtot = -18181.0945
> BOND = 2952.8501 ANGLE = 12115.7213 DIHED = 11152.3764
> 1-4 NB = 3234.7249 1-4 EEL = -47672.7913 VDWAALS = -8917.7466
> EELEC = 8953.7707 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 411.5360 VIRIAL = 1834.5450 VOLUME = 573105.0781
> Density = 0.3686
> ------------------------------------------------------------------------------
>
>
> NSTEP = 71000 TIME(PS) = 142.000 TEMP(K) = 297.36 PRESS = -144.8
> Etot = -1622.7163 EKtot = 16841.1113 EPtot = -18463.8276
> BOND = 2913.8978 ANGLE = 12003.2930 DIHED = 11101.7473
> 1-4 NB = 3283.6827 1-4 EEL = -47696.6559 VDWAALS = -8948.9630
> EELEC = 8879.1705 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 450.7365 VIRIAL = 2236.7989 VOLUME = 571380.3406
> Density = 0.3697
> ------------------------------------------------------------------------------
>
>
> NSTEP = 72000 TIME(PS) = 144.000 TEMP(K) = 294.62 PRESS = -93.9
> Etot = -1590.3782 EKtot = 16685.9688 EPtot = -18276.3469
> BOND = 2876.4532 ANGLE = 12043.1314 DIHED = 11233.6400
> 1-4 NB = 3253.2198 1-4 EEL = -47659.9417 VDWAALS = -8881.3628
> EELEC = 8858.5132 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 458.0297 VIRIAL = 1611.7417 VOLUME = 569097.5394
> Density = 0.3712
> ------------------------------------------------------------------------------
>
>
> NSTEP = 73000 TIME(PS) = 146.000 TEMP(K) = 297.86 PRESS = -193.4
> Etot = -1377.2668 EKtot = 16869.4492 EPtot = -18246.7161
> BOND = 2906.8393 ANGLE = 12121.9114 DIHED = 11146.1262
> 1-4 NB = 3275.0122 1-4 EEL = -47734.6323 VDWAALS = -8865.7654
> EELEC = 8903.7926 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 471.7384 VIRIAL = 2840.7215 VOLUME = 567235.5862
> Density = 0.3724
> ------------------------------------------------------------------------------
>
>
> NSTEP = 74000 TIME(PS) = 148.000 TEMP(K) = 295.50 PRESS = -158.1
> Etot = -1492.6289 EKtot = 16735.3926 EPtot = -18228.0214
> BOND = 2998.3002 ANGLE = 12128.8126 DIHED = 11130.0484
> 1-4 NB = 3250.9778 1-4 EEL = -47700.5454 VDWAALS = -8933.5287
> EELEC = 8897.9136 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 458.7090 VIRIAL = 2389.0334 VOLUME = 565416.2537
> Density = 0.3736
> ------------------------------------------------------------------------------
>
>
> NSTEP = 75000 TIME(PS) = 150.000 TEMP(K) = 297.92 PRESS = -258.2
> Etot = -1737.2378 EKtot = 16872.4453 EPtot = -18609.6831
> BOND = 2964.7506 ANGLE = 11908.4194 DIHED = 11057.5255
> 1-4 NB = 3233.0329 1-4 EEL = -47658.0372 VDWAALS = -8997.3836
> EELEC = 8882.0092 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 464.8790 VIRIAL = 3602.8976 VOLUME = 562914.1321
> Density = 0.3752
> ------------------------------------------------------------------------------
>
>
> NSTEP = 76000 TIME(PS) = 152.000 TEMP(K) = 298.59 PRESS = -200.7
> Etot = -1511.6962 EKtot = 16910.5020 EPtot = -18422.1981
> BOND = 2976.1858 ANGLE = 12164.3779 DIHED = 11122.7796
> 1-4 NB = 3214.9353 1-4 EEL = -47695.4353 VDWAALS = -9030.6921
> EELEC = 8825.6507 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 422.1827 VIRIAL = 2852.5188 VOLUME = 560824.9964
> Density = 0.3766
> ------------------------------------------------------------------------------
>
>
> NSTEP = 77000 TIME(PS) = 154.000 TEMP(K) = 298.85 PRESS = -108.3
> Etot = -1463.8099 EKtot = 16925.2676 EPtot = -18389.0775
> BOND = 2942.3716 ANGLE = 12096.0844 DIHED = 11136.2397
> 1-4 NB = 3223.1426 1-4 EEL = -47701.8054 VDWAALS = -8856.1711
> EELEC = 8771.0607 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 427.8432 VIRIAL = 1733.7622 VOLUME = 558696.3577
> Density = 0.3781
> ------------------------------------------------------------------------------
>
>
> NSTEP = 78000 TIME(PS) = 156.000 TEMP(K) = 299.30 PRESS = -216.9
> Etot = -1314.1979 EKtot = 16950.6855 EPtot = -18264.8834
> BOND = 2974.2354 ANGLE = 12194.0187 DIHED = 11101.9739
> 1-4 NB = 3251.1319 1-4 EEL = -47651.2144 VDWAALS = -8934.3801
> EELEC = 8799.3513 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 452.2013 VIRIAL = 3059.9082 VOLUME = 556809.9391
> Density = 0.3793
> ------------------------------------------------------------------------------
>
>
> NSTEP = 79000 TIME(PS) = 158.000 TEMP(K) = 298.64 PRESS = -155.6
> Etot = -1370.0557 EKtot = 16913.2578 EPtot = -18283.3135
> BOND = 3076.3874 ANGLE = 12018.9091 DIHED = 11138.7953
> 1-4 NB = 3248.7578 1-4 EEL = -47639.4857 VDWAALS = -8960.0637
> EELEC = 8833.3864 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 445.7120 VIRIAL = 2309.1298 VOLUME = 554825.4164
> Density = 0.3807
> ------------------------------------------------------------------------------
>
>
> NSTEP = 80000 TIME(PS) = 160.000 TEMP(K) = 299.35 PRESS = -89.6
> Etot = -1372.7697 EKtot = 16953.6172 EPtot = -18326.3869
> BOND = 2885.7588 ANGLE = 12158.3256 DIHED = 11153.3666
> 1-4 NB = 3231.0373 1-4 EEL = -47659.0042 VDWAALS = -8843.4382
> EELEC = 8747.5672 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 447.7564 VIRIAL = 1516.6762 VOLUME = 552602.5552
> Density = 0.3822
> ------------------------------------------------------------------------------
>
>
> NSTEP = 81000 TIME(PS) = 162.000 TEMP(K) = 298.29 PRESS = -83.5
> Etot = -1485.4221 EKtot = 16893.6855 EPtot = -18379.1077
> BOND = 2900.2159 ANGLE = 12118.4430 DIHED = 11088.2050
> 1-4 NB = 3284.0375 1-4 EEL = -47742.7494 VDWAALS = -8879.0961
> EELEC = 8851.8364 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 474.0557 VIRIAL = 1466.0689 VOLUME = 550319.5843
> Density = 0.3838
> ------------------------------------------------------------------------------
>
>
> NSTEP = 82000 TIME(PS) = 164.000 TEMP(K) = 295.36 PRESS = -35.2
> Etot = -1621.5055 EKtot = 16727.7617 EPtot = -18349.2672
> BOND = 2890.0266 ANGLE = 12020.6438 DIHED = 11207.5254
> 1-4 NB = 3248.8696 1-4 EEL = -47602.2068 VDWAALS = -8872.2551
> EELEC = 8758.1293 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 431.1448 VIRIAL = 848.4017 VOLUME = 548916.7171
> Density = 0.3848
> ------------------------------------------------------------------------------
>
>
> NSTEP = 83000 TIME(PS) = 166.000 TEMP(K) = 299.93 PRESS = -101.5
> Etot = -1493.7098 EKtot = 16986.7031 EPtot = -18480.4130
> BOND = 2936.5655 ANGLE = 11973.7234 DIHED = 11152.7409
> 1-4 NB = 3259.9308 1-4 EEL = -47611.1356 VDWAALS = -8873.2698
> EELEC = 8681.0320 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 435.3287 VIRIAL = 1634.8034 VOLUME = 547143.5709
> Density = 0.3860
> ------------------------------------------------------------------------------
>
>
> NSTEP = 84000 TIME(PS) = 168.000 TEMP(K) = 297.40 PRESS = -69.4
> Etot = -1458.8776 EKtot = 16843.2793 EPtot = -18302.1569
> BOND = 2944.5903 ANGLE = 12196.0602 DIHED = 11171.5217
> 1-4 NB = 3262.5997 1-4 EEL = -47700.5602 VDWAALS = -8964.2012
> EELEC = 8787.8327 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 427.2710 VIRIAL = 1244.4116 VOLUME = 545162.7579
> Density = 0.3875
> ------------------------------------------------------------------------------
>
>
> NSTEP = 85000 TIME(PS) = 170.000 TEMP(K) = 297.70 PRESS = -128.8
> Etot = -1516.5481 EKtot = 16860.3691 EPtot = -18376.9172
> BOND = 2935.6349 ANGLE = 12018.6980 DIHED = 11163.1686
> 1-4 NB = 3268.1590 1-4 EEL = -47626.0885 VDWAALS = -8949.1694
> EELEC = 8812.6801 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 464.4359 VIRIAL = 1975.2508 VOLUME = 543334.7034
> Density = 0.3888
> ------------------------------------------------------------------------------
>
>
> NSTEP = 86000 TIME(PS) = 172.000 TEMP(K) = 294.85 PRESS = -153.9
> Etot = -1775.4557 EKtot = 16698.5664 EPtot = -18474.0221
> BOND = 2927.6871 ANGLE = 12078.2747 DIHED = 11128.9961
> 1-4 NB = 3263.7914 1-4 EEL = -47736.3157 VDWAALS = -8891.1519
> EELEC = 8754.6961 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 443.0511 VIRIAL = 2239.7727 VOLUME = 540782.0735
> Density = 0.3906
> ------------------------------------------------------------------------------
>
>
> NSTEP = 87000 TIME(PS) = 174.000 TEMP(K) = 297.78 PRESS = -189.5
> Etot = -1419.9488 EKtot = 16864.9531 EPtot = -18284.9019
> BOND = 3005.5259 ANGLE = 12070.0788 DIHED = 11179.6050
> 1-4 NB = 3276.2815 1-4 EEL = -47777.5243 VDWAALS = -8907.1669
> EELEC = 8868.2980 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 448.6522 VIRIAL = 2651.1249 VOLUME = 538300.3457
> Density = 0.3924
> ------------------------------------------------------------------------------
>
>
> NSTEP = 88000 TIME(PS) = 176.000 TEMP(K) = 300.43 PRESS = -200.6
> Etot = -1442.6061 EKtot = 17015.0820 EPtot = -18457.6881
> BOND = 2956.3748 ANGLE = 11994.5923 DIHED = 11132.8901
> 1-4 NB = 3261.0547 1-4 EEL = -47576.2691 VDWAALS = -8997.6493
> EELEC = 8771.3184 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 442.5203 VIRIAL = 2766.5833 VOLUME = 536478.6634
> Density = 0.3937
> ------------------------------------------------------------------------------
>
>
> NSTEP = 89000 TIME(PS) = 178.000 TEMP(K) = 296.06 PRESS = -169.0
> Etot = -1454.6607 EKtot = 16767.2500 EPtot = -18221.9107
> BOND = 3014.8260 ANGLE = 12128.9406 DIHED = 11251.8651
> 1-4 NB = 3271.0740 1-4 EEL = -47735.2786 VDWAALS = -8961.5962
> EELEC = 8808.2585 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 455.2124 VIRIAL = 2406.3045 VOLUME = 534806.4246
> Density = 0.3950
> ------------------------------------------------------------------------------
>
>
> NSTEP = 90000 TIME(PS) = 180.000 TEMP(K) = 297.44 PRESS = -81.5
> Etot = -1449.4456 EKtot = 16845.5938 EPtot = -18295.0393
> BOND = 3027.2044 ANGLE = 12106.2360 DIHED = 11100.9861
> 1-4 NB = 3247.0061 1-4 EEL = -47651.7374 VDWAALS = -8893.6452
> EELEC = 8768.9108 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 443.5941 VIRIAL = 1381.7734 VOLUME = 533171.1810
> Density = 0.3962
> ------------------------------------------------------------------------------
>
>
> NSTEP = 91000 TIME(PS) = 182.000 TEMP(K) = 298.41 PRESS = -130.8
> Etot = -1578.4397 EKtot = 16900.6191 EPtot = -18479.0589
> BOND = 2932.8980 ANGLE = 11818.1709 DIHED = 11196.9917
> 1-4 NB = 3269.2883 1-4 EEL = -47520.6405 VDWAALS = -8871.9796
> EELEC = 8696.2123 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 481.4047 VIRIAL = 1982.2735 VOLUME = 531335.6708
> Density = 0.3975
> ------------------------------------------------------------------------------
>
>
> NSTEP = 92000 TIME(PS) = 184.000 TEMP(K) = 293.25 PRESS = -44.5
> Etot = -1677.3353 EKtot = 16608.3906 EPtot = -18285.7259
> BOND = 2951.0572 ANGLE = 12152.5635 DIHED = 11167.5079
> 1-4 NB = 3287.9924 1-4 EEL = -47741.9826 VDWAALS = -8788.6887
> EELEC = 8685.8244 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 404.3339 VIRIAL = 913.1987 VOLUME = 529324.5213
> Density = 0.3990
> ------------------------------------------------------------------------------
>
>
> NSTEP = 93000 TIME(PS) = 186.000 TEMP(K) = 296.47 PRESS = -118.1
> Etot = -1640.2782 EKtot = 16790.6074 EPtot = -18430.8857
> BOND = 2894.3355 ANGLE = 11959.7616 DIHED = 11219.1981
> 1-4 NB = 3308.5202 1-4 EEL = -47575.8245 VDWAALS = -8933.5073
> EELEC = 8696.6308 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 463.3700 VIRIAL = 1806.9781 VOLUME = 527057.4644
> Density = 0.4008
> ------------------------------------------------------------------------------
>
>
> NSTEP = 94000 TIME(PS) = 188.000 TEMP(K) = 296.83 PRESS = -60.1
> Etot = -1674.3867 EKtot = 16811.1055 EPtot = -18485.4921
> BOND = 2910.2575 ANGLE = 12005.1524 DIHED = 11206.5571
> 1-4 NB = 3255.2524 1-4 EEL = -47551.3099 VDWAALS = -9004.3381
> EELEC = 8692.9366 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 441.5674 VIRIAL = 1123.1660 VOLUME = 525570.7750
> Density = 0.4019
> ------------------------------------------------------------------------------
>
>
> NSTEP = 95000 TIME(PS) = 190.000 TEMP(K) = 297.87 PRESS = -49.6
> Etot = -1535.2490 EKtot = 16869.9297 EPtot = -18405.1787
> BOND = 3010.5748 ANGLE = 11972.6878 DIHED = 11217.4211
> 1-4 NB = 3276.6738 1-4 EEL = -47644.6753 VDWAALS = -8910.2012
> EELEC = 8672.3402 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 435.5559 VIRIAL = 997.0739 VOLUME = 524160.8947
> Density = 0.4030
> ------------------------------------------------------------------------------
>
>
> NSTEP = 96000 TIME(PS) = 192.000 TEMP(K) = 299.69 PRESS = -163.3
> Etot = -1514.3813 EKtot = 16973.0586 EPtot = -18487.4399
> BOND = 2905.2161 ANGLE = 12119.5387 DIHED = 11127.4453
> 1-4 NB = 3228.4573 1-4 EEL = -47605.7166 VDWAALS = -8920.5138
> EELEC = 8658.1331 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 458.5624 VIRIAL = 2300.9670 VOLUME = 522404.5413
> Density = 0.4043
> ------------------------------------------------------------------------------
>
>
> NSTEP = 97000 TIME(PS) = 194.000 TEMP(K) = 296.83 PRESS = -43.4
> Etot = -1713.9789 EKtot = 16811.1348 EPtot = -18525.1137
> BOND = 2936.8311 ANGLE = 12099.8260 DIHED = 11162.7002
> 1-4 NB = 3245.9889 1-4 EEL = -47763.1440 VDWAALS = -8949.3730
> EELEC = 8742.0569 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 415.7399 VIRIAL = 903.6609 VOLUME = 520288.6832
> Density = 0.4060
> ------------------------------------------------------------------------------
>
>
> NSTEP = 98000 TIME(PS) = 196.000 TEMP(K) = 297.92 PRESS = -79.5
> Etot = -1642.7545 EKtot = 16872.8770 EPtot = -18515.6315
> BOND = 2980.7235 ANGLE = 11915.8184 DIHED = 11149.0476
> 1-4 NB = 3267.7242 1-4 EEL = -47625.1899 VDWAALS = -8889.3827
> EELEC = 8685.6274 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 439.0656 VIRIAL = 1329.2444 VOLUME = 518629.6518
> Density = 0.4073
> ------------------------------------------------------------------------------
>
>
> NSTEP = 99000 TIME(PS) = 198.000 TEMP(K) = 297.88 PRESS = -138.7
> Etot = -1598.8893 EKtot = 16870.2773 EPtot = -18469.1666
> BOND = 2981.3862 ANGLE = 12108.5974 DIHED = 11182.2438
> 1-4 NB = 3258.3758 1-4 EEL = -47751.6265 VDWAALS = -9000.4876
> EELEC = 8752.3441 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 441.3528 VIRIAL = 1990.1376 VOLUME = 517141.9289
> Density = 0.4084
> ------------------------------------------------------------------------------
>
>
> NSTEP = 100000 TIME(PS) = 200.000 TEMP(K) = 299.87 PRESS = -81.9
> Etot = -1467.2276 EKtot = 16983.2285 EPtot = -18450.4561
> BOND = 2939.9080 ANGLE = 12126.0957 DIHED = 11180.4258
> 1-4 NB = 3267.3924 1-4 EEL = -47666.8543 VDWAALS = -8954.7927
> EELEC = 8657.3690 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 438.7197 VIRIAL = 1350.5646 VOLUME = 515447.5036
> Density = 0.4098
> ------------------------------------------------------------------------------
>
>
> NSTEP = 101000 TIME(PS) = 202.000 TEMP(K) = 301.86 PRESS = -155.7
> Etot = -1486.5211 EKtot = 17095.8691 EPtot = -18582.3902
> BOND = 2937.1174 ANGLE = 11945.1604 DIHED = 11163.1319
> 1-4 NB = 3250.7358 1-4 EEL = -47567.8177 VDWAALS = -8965.7819
> EELEC = 8655.0639 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 452.2955 VIRIAL = 2179.8960 VOLUME = 513958.8268
> Density = 0.4110
> ------------------------------------------------------------------------------
>
>
> NSTEP = 102000 TIME(PS) = 204.000 TEMP(K) = 300.06 PRESS = -128.5
> Etot = -1342.7032 EKtot = 16993.8789 EPtot = -18336.5821
> BOND = 2992.1913 ANGLE = 12202.4140 DIHED = 11176.6472
> 1-4 NB = 3267.6101 1-4 EEL = -47698.1657 VDWAALS = -8979.2288
> EELEC = 8701.9497 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 446.9259 VIRIAL = 1867.2534 VOLUME = 511831.5704
> Density = 0.4127
> ------------------------------------------------------------------------------
>
>
> NSTEP = 103000 TIME(PS) = 206.000 TEMP(K) = 297.79 PRESS = -128.8
> Etot = -1520.7130 EKtot = 16865.1367 EPtot = -18385.8497
> BOND = 3071.3755 ANGLE = 12220.2393 DIHED = 11137.9726
> 1-4 NB = 3265.9882 1-4 EEL = -47719.3106 VDWAALS = -9037.6747
> EELEC = 8675.5601 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 485.8155 VIRIAL = 1904.4756 VOLUME = 510192.7302
> Density = 0.4140
> ------------------------------------------------------------------------------
>
>
> NSTEP = 104000 TIME(PS) = 208.000 TEMP(K) = 298.89 PRESS = -75.1
> Etot = -1559.4304 EKtot = 16927.7129 EPtot = -18487.1433
> BOND = 2978.5606 ANGLE = 12067.7770 DIHED = 11202.6061
> 1-4 NB = 3282.8469 1-4 EEL = -47674.2533 VDWAALS = -8936.9145
> EELEC = 8592.2338 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 470.2211 VIRIAL = 1294.2303 VOLUME = 508054.0186
> Density = 0.4158
> ------------------------------------------------------------------------------
>
>
> NSTEP = 105000 TIME(PS) = 210.000 TEMP(K) = 296.31 PRESS = -91.7
> Etot = -1895.0235 EKtot = 16781.7090 EPtot = -18676.7325
> BOND = 2971.6461 ANGLE = 11963.5334 DIHED = 11145.9044
> 1-4 NB = 3258.9839 1-4 EEL = -47630.0800 VDWAALS = -9000.4896
> EELEC = 8613.7693 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 425.0713 VIRIAL = 1427.4729 VOLUME = 506285.2522
> Density = 0.4172
> ------------------------------------------------------------------------------
>
>
> NSTEP = 106000 TIME(PS) = 212.000 TEMP(K) = 298.77 PRESS = -321.5
> Etot = -1410.1255 EKtot = 16920.9355 EPtot = -18331.0611
> BOND = 3029.0104 ANGLE = 12086.5110 DIHED = 11205.6448
> 1-4 NB = 3281.7769 1-4 EEL = -47649.6218 VDWAALS = -9022.9512
> EELEC = 8738.5688 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 440.1359 VIRIAL = 3941.9537 VOLUME = 504462.4890
> Density = 0.4187
> ------------------------------------------------------------------------------
>
>
> NSTEP = 107000 TIME(PS) = 214.000 TEMP(K) = 300.13 PRESS = -76.0
> Etot = -1508.7587 EKtot = 16997.6992 EPtot = -18506.4580
> BOND = 2955.1746 ANGLE = 12044.2766 DIHED = 11240.3598
> 1-4 NB = 3277.1278 1-4 EEL = -47637.0125 VDWAALS = -9021.6736
> EELEC = 8635.2894 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 461.0934 VIRIAL = 1286.1702 VOLUME = 502672.7735
> Density = 0.4202
> ------------------------------------------------------------------------------
>
>
> NSTEP = 108000 TIME(PS) = 216.000 TEMP(K) = 297.74 PRESS = -238.9
> Etot = -1640.1991 EKtot = 16862.5977 EPtot = -18502.7967
> BOND = 2996.4289 ANGLE = 12157.6869 DIHED = 11269.1970
> 1-4 NB = 3247.3014 1-4 EEL = -47681.4141 VDWAALS = -9111.0262
> EELEC = 8619.0294 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 441.0562 VIRIAL = 3027.1540 VOLUME = 501456.7070
> Density = 0.4212
> ------------------------------------------------------------------------------
>
>
> NSTEP = 109000 TIME(PS) = 218.000 TEMP(K) = 297.62 PRESS = -20.9
> Etot = -1807.5386 EKtot = 16855.4961 EPtot = -18663.0346
> BOND = 3025.0470 ANGLE = 11903.2241 DIHED = 11183.4483
> 1-4 NB = 3221.9981 1-4 EEL = -47603.6261 VDWAALS = -8922.2572
> EELEC = 8529.1310 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 440.6222 VIRIAL = 665.8427 VOLUME = 499255.5464
> Density = 0.4231
> ------------------------------------------------------------------------------
>
>
> NSTEP = 110000 TIME(PS) = 220.000 TEMP(K) = 298.90 PRESS = -22.7
> Etot = -1645.8893 EKtot = 16928.4727 EPtot = -18574.3619
> BOND = 2969.8639 ANGLE = 11958.5631 DIHED = 11171.9916
> 1-4 NB = 3250.1167 1-4 EEL = -47564.3081 VDWAALS = -8973.2036
> EELEC = 8612.6144 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 476.4663 VIRIAL = 720.0683 VOLUME = 497586.5197
> Density = 0.4245
> ------------------------------------------------------------------------------
>
>
> NSTEP = 111000 TIME(PS) = 222.000 TEMP(K) = 296.43 PRESS = -144.3
> Etot = -1732.7210 EKtot = 16788.2227 EPtot = -18520.9436
> BOND = 2967.0091 ANGLE = 12046.2765 DIHED = 11126.7134
> 1-4 NB = 3276.2191 1-4 EEL = -47620.5260 VDWAALS = -8985.0778
> EELEC = 8668.4422 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 438.2271 VIRIAL = 1982.9261 VOLUME = 495796.4827
> Density = 0.4260
> ------------------------------------------------------------------------------
>
>
> NSTEP = 112000 TIME(PS) = 224.000 TEMP(K) = 302.93 PRESS = -107.7
> Etot = -1470.4691 EKtot = 17156.5723 EPtot = -18627.0414
> BOND = 2960.0533 ANGLE = 12055.0262 DIHED = 11217.0757
> 1-4 NB = 3227.6745 1-4 EEL = -47644.3762 VDWAALS = -9011.8087
> EELEC = 8569.3138 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 448.9079 VIRIAL = 1596.5792 VOLUME = 493549.5290
> Density = 0.4280
> ------------------------------------------------------------------------------
>
>
> NSTEP = 113000 TIME(PS) = 226.000 TEMP(K) = 299.76 PRESS = -387.8
> Etot = -1686.1391 EKtot = 16977.0586 EPtot = -18663.1977
> BOND = 2937.9275 ANGLE = 12002.2956 DIHED = 11186.7805
> 1-4 NB = 3223.2657 1-4 EEL = -47580.9402 VDWAALS = -9047.0375
> EELEC = 8614.5107 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 445.1333 VIRIAL = 4562.5310 VOLUME = 491785.3052
> Density = 0.4295
> ------------------------------------------------------------------------------
>
>
> NSTEP = 114000 TIME(PS) = 228.000 TEMP(K) = 297.00 PRESS = -56.8
> Etot = -1716.9904 EKtot = 16820.4043 EPtot = -18537.3947
> BOND = 2923.6398 ANGLE = 11998.2961 DIHED = 11195.4142
> 1-4 NB = 3256.0012 1-4 EEL = -47606.4117 VDWAALS = -8891.5929
> EELEC = 8587.2586 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 437.3751 VIRIAL = 1037.8175 VOLUME = 489666.4968
> Density = 0.4314
> ------------------------------------------------------------------------------
>
>
> NSTEP = 115000 TIME(PS) = 230.000 TEMP(K) = 295.16 PRESS = -70.7
> Etot = -1952.3284 EKtot = 16716.5234 EPtot = -18668.8519
> BOND = 2872.4668 ANGLE = 12010.9299 DIHED = 11183.4030
> 1-4 NB = 3266.1167 1-4 EEL = -47662.7434 VDWAALS = -8971.1705
> EELEC = 8632.1456 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 471.6080 VIRIAL = 1215.4866 VOLUME = 487343.7475
> Density = 0.4334
> ------------------------------------------------------------------------------
>
>
> NSTEP = 116000 TIME(PS) = 232.000 TEMP(K) = 301.18 PRESS = -153.6
> Etot = -1621.1520 EKtot = 17057.1641 EPtot = -18678.3160
> BOND = 2983.2509 ANGLE = 11933.8844 DIHED = 11182.6948
> 1-4 NB = 3232.5181 1-4 EEL = -47677.1804 VDWAALS = -8950.6555
> EELEC = 8617.1718 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 433.3661 VIRIAL = 2044.0864 VOLUME = 485597.4354
> Density = 0.4350
> ------------------------------------------------------------------------------
>
>
> NSTEP = 117000 TIME(PS) = 234.000 TEMP(K) = 300.83 PRESS = -110.6
> Etot = -1437.4263 EKtot = 17037.3887 EPtot = -18474.8149
> BOND = 2969.5724 ANGLE = 12039.6826 DIHED = 11216.1004
> 1-4 NB = 3267.9072 1-4 EEL = -47705.1076 VDWAALS = -8894.1328
> EELEC = 8631.1629 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 460.6033 VIRIAL = 1615.6520 VOLUME = 483720.3214
> Density = 0.4367
> ------------------------------------------------------------------------------
>
>
> NSTEP = 118000 TIME(PS) = 236.000 TEMP(K) = 300.07 PRESS = -125.9
> Etot = -1380.5602 EKtot = 16994.4102 EPtot = -18374.9704
> BOND = 2991.8399 ANGLE = 12111.9192 DIHED = 11187.2428
> 1-4 NB = 3241.5102 1-4 EEL = -47635.1144 VDWAALS = -8847.7711
> EELEC = 8575.4031 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 443.9019 VIRIAL = 1753.6421 VOLUME = 481682.9594
> Density = 0.4385
> ------------------------------------------------------------------------------
>
>
> NSTEP = 119000 TIME(PS) = 238.000 TEMP(K) = 299.93 PRESS = -89.8
> Etot = -1404.8494 EKtot = 16986.4395 EPtot = -18391.2889
> BOND = 2995.3079 ANGLE = 12018.8238 DIHED = 11164.0807
> 1-4 NB = 3274.3666 1-4 EEL = -47586.1436 VDWAALS = -8851.7053
> EELEC = 8593.9811 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 437.3837 VIRIAL = 1366.2862 VOLUME = 479250.7906
> Density = 0.4407
> ------------------------------------------------------------------------------
>
>
> NSTEP = 120000 TIME(PS) = 240.000 TEMP(K) = 299.70 PRESS = -258.8
> Etot = -1498.7549 EKtot = 16973.5508 EPtot = -18472.3057
> BOND = 2954.4458 ANGLE = 12048.6661 DIHED = 11183.6154
> 1-4 NB = 3290.7296 1-4 EEL = -47659.8439 VDWAALS = -8921.9119
> EELEC = 8631.9932 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 443.4911 VIRIAL = 3108.6077 VOLUME = 476930.8389
> Density = 0.4429
> ------------------------------------------------------------------------------
>
>
> NSTEP = 121000 TIME(PS) = 242.000 TEMP(K) = 300.18 PRESS = -160.5
> Etot = -1550.5304 EKtot = 17000.4199 EPtot = -18550.9503
> BOND = 2960.5075 ANGLE = 12029.9446 DIHED = 11216.4225
> 1-4 NB = 3284.2021 1-4 EEL = -47703.1190 VDWAALS = -8976.3473
> EELEC = 8637.4392 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 417.0300 VIRIAL = 2061.3892 VOLUME = 474650.7218
> Density = 0.4450
> ------------------------------------------------------------------------------
>
>
> NSTEP = 122000 TIME(PS) = 244.000 TEMP(K) = 299.33 PRESS = -269.9
> Etot = -1613.9422 EKtot = 16952.5332 EPtot = -18566.4754
> BOND = 3005.9345 ANGLE = 12077.6603 DIHED = 11172.4447
> 1-4 NB = 3206.4006 1-4 EEL = -47607.7984 VDWAALS = -9002.4271
> EELEC = 8581.3099 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 464.6004 VIRIAL = 3217.4129 VOLUME = 472313.0953
> Density = 0.4472
> ------------------------------------------------------------------------------
>
>
> NSTEP = 123000 TIME(PS) = 246.000 TEMP(K) = 297.50 PRESS = -38.0
> Etot = -1850.6819 EKtot = 16848.9824 EPtot = -18699.6643
> BOND = 2955.9439 ANGLE = 11790.0664 DIHED = 11238.0158
> 1-4 NB = 3273.2347 1-4 EEL = -47512.6681 VDWAALS = -8942.8348
> EELEC = 8498.5778 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 429.0946 VIRIAL = 814.6655 VOLUME = 470019.1849
> Density = 0.4494
> ------------------------------------------------------------------------------
>
>
> NSTEP = 124000 TIME(PS) = 248.000 TEMP(K) = 296.80 PRESS = -110.2
> Etot = -1815.5029 EKtot = 16809.2949 EPtot = -18624.7978
> BOND = 2911.5168 ANGLE = 12062.6859 DIHED = 11187.3609
> 1-4 NB = 3280.2267 1-4 EEL = -47676.1390 VDWAALS = -8907.5815
> EELEC = 8517.1324 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 428.1208 VIRIAL = 1542.1993 VOLUME = 468095.3541
> Density = 0.4512
> ------------------------------------------------------------------------------
>
>
> NSTEP = 125000 TIME(PS) = 250.000 TEMP(K) = 298.76 PRESS = -106.2
> Etot = -1627.1782 EKtot = 16920.3789 EPtot = -18547.5571
> BOND = 3042.4972 ANGLE = 12079.0173 DIHED = 11182.2417
> 1-4 NB = 3249.0591 1-4 EEL = -47690.5221 VDWAALS = -9003.7278
> EELEC = 8593.8775 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 450.9999 VIRIAL = 1520.0520 VOLUME = 466391.7851
> Density = 0.4529
> ------------------------------------------------------------------------------
>
>
> NSTEP = 126000 TIME(PS) = 252.000 TEMP(K) = 298.44 PRESS = -122.7
> Etot = -1749.6140 EKtot = 16902.1270 EPtot = -18651.7409
> BOND = 2955.6116 ANGLE = 11995.4878 DIHED = 11196.5326
> 1-4 NB = 3279.3999 1-4 EEL = -47637.5483 VDWAALS = -9005.2753
> EELEC = 8564.0508 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 443.4232 VIRIAL = 1674.3537 VOLUME = 464623.9849
> Density = 0.4546
> ------------------------------------------------------------------------------
>
>
> NSTEP = 127000 TIME(PS) = 254.000 TEMP(K) = 300.79 PRESS = -167.3
> Etot = -1789.3220 EKtot = 17035.2109 EPtot = -18824.5329
> BOND = 2982.3608 ANGLE = 11888.5012 DIHED = 11189.0855
> 1-4 NB = 3235.8437 1-4 EEL = -47660.1528 VDWAALS = -8956.7729
> EELEC = 8496.6016 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 423.4990 VIRIAL = 2092.4303 VOLUME = 462119.9687
> Density = 0.4571
> ------------------------------------------------------------------------------
>
>
> NSTEP = 128000 TIME(PS) = 256.000 TEMP(K) = 298.56 PRESS = -182.0
> Etot = -1580.0130 EKtot = 16909.0293 EPtot = -18489.0423
> BOND = 2906.2601 ANGLE = 12196.6926 DIHED = 11134.9716
> 1-4 NB = 3260.1829 1-4 EEL = -47652.4290 VDWAALS = -8951.7628
> EELEC = 8617.0424 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 460.8074 VIRIAL = 2267.9900 VOLUME = 459827.1073
> Density = 0.4594
> ------------------------------------------------------------------------------
>
>
> NSTEP = 129000 TIME(PS) = 258.000 TEMP(K) = 297.01 PRESS = -125.6
> Etot = -1794.7427 EKtot = 16821.4277 EPtot = -18616.1704
> BOND = 2915.8664 ANGLE = 12008.1956 DIHED = 11248.3386
> 1-4 NB = 3259.2937 1-4 EEL = -47606.1968 VDWAALS = -8948.4358
> EELEC = 8506.7677 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 422.7848 VIRIAL = 1664.4483 VOLUME = 457905.9879
> Density = 0.4613
> ------------------------------------------------------------------------------
>
>
> NSTEP = 130000 TIME(PS) = 260.000 TEMP(K) = 301.26 PRESS = -49.3
> Etot = -1550.6390 EKtot = 17061.6152 EPtot = -18612.2543
> BOND = 2858.4851 ANGLE = 12054.4670 DIHED = 11245.7111
> 1-4 NB = 3289.0349 1-4 EEL = -47662.3627 VDWAALS = -8966.5538
> EELEC = 8568.9641 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 450.3443 VIRIAL = 934.6706 VOLUME = 455454.8958
> Density = 0.4638
> ------------------------------------------------------------------------------
>
>
> NSTEP = 131000 TIME(PS) = 262.000 TEMP(K) = 296.06 PRESS = -176.3
> Etot = -1929.5268 EKtot = 16767.2891 EPtot = -18696.8159
> BOND = 3010.8088 ANGLE = 12068.7803 DIHED = 11162.1665
> 1-4 NB = 3252.7611 1-4 EEL = -47730.2961 VDWAALS = -8994.2573
> EELEC = 8533.2208 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 480.1041 VIRIAL = 2206.8071 VOLUME = 453674.6781
> Density = 0.4656
> ------------------------------------------------------------------------------
>
>
> NSTEP = 132000 TIME(PS) = 264.000 TEMP(K) = 298.18 PRESS = -46.4
> Etot = -1903.1348 EKtot = 16887.5879 EPtot = -18790.7227
> BOND = 2888.1896 ANGLE = 11942.7641 DIHED = 11146.7783
> 1-4 NB = 3279.8465 1-4 EEL = -47602.2972 VDWAALS = -8957.3708
> EELEC = 8511.3669 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 418.4454 VIRIAL = 871.0777 VOLUME = 451931.9209
> Density = 0.4674
> ------------------------------------------------------------------------------
>
>
> NSTEP = 133000 TIME(PS) = 266.000 TEMP(K) = 297.78 PRESS = -90.6
> Etot = -1716.8727 EKtot = 16864.6211 EPtot = -18581.4938
> BOND = 2979.8666 ANGLE = 12019.1807 DIHED = 11266.7536
> 1-4 NB = 3232.9836 1-4 EEL = -47549.5837 VDWAALS = -9050.9951
> EELEC = 8520.3006 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 439.7844 VIRIAL = 1320.0175 VOLUME = 449886.1313
> Density = 0.4695
> ------------------------------------------------------------------------------
>
>
> NSTEP = 134000 TIME(PS) = 268.000 TEMP(K) = 297.31 PRESS = -3.8
> Etot = -1861.1068 EKtot = 16838.0488 EPtot = -18699.1556
> BOND = 2873.0526 ANGLE = 12014.9889 DIHED = 11151.3199
> 1-4 NB = 3255.4486 1-4 EEL = -47557.2301 VDWAALS = -8922.6157
> EELEC = 8485.8803 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 453.1214 VIRIAL = 489.6379 VOLUME = 447847.9422
> Density = 0.4716
> ------------------------------------------------------------------------------
>
>
> NSTEP = 135000 TIME(PS) = 270.000 TEMP(K) = 297.78 PRESS = -114.0
> Etot = -1812.2959 EKtot = 16864.8496 EPtot = -18677.1455
> BOND = 2984.8790 ANGLE = 12027.4044 DIHED = 11258.7936
> 1-4 NB = 3251.7607 1-4 EEL = -47563.5628 VDWAALS = -9087.8051
> EELEC = 8451.3846 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 439.9235 VIRIAL = 1536.0200 VOLUME = 445494.2926
> Density = 0.4741
> ------------------------------------------------------------------------------
>
>
> NSTEP = 136000 TIME(PS) = 272.000 TEMP(K) = 298.67 PRESS = 60.7
> Etot = -1784.3197 EKtot = 16915.4063 EPtot = -18699.7259
> BOND = 2951.9069 ANGLE = 11967.1321 DIHED = 11316.8553
> 1-4 NB = 3221.9296 1-4 EEL = -47574.0331 VDWAALS = -9045.9333
> EELEC = 8462.4166 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 452.2605 VIRIAL = -130.0319 VOLUME = 444085.6522
> Density = 0.4756
> ------------------------------------------------------------------------------
>
>
> NSTEP = 137000 TIME(PS) = 274.000 TEMP(K) = 295.18 PRESS = -71.4
> Etot = -2155.3291 EKtot = 16717.7832 EPtot = -18873.1123
> BOND = 2897.8284 ANGLE = 11931.9809 DIHED = 11261.2887
> 1-4 NB = 3257.6665 1-4 EEL = -47608.8099 VDWAALS = -9068.6054
> EELEC = 8455.5384 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 426.5153 VIRIAL = 1108.2976 VOLUME = 441945.6060
> Density = 0.4779
> ------------------------------------------------------------------------------
>
>
> NSTEP = 138000 TIME(PS) = 276.000 TEMP(K) = 297.77 PRESS = -161.8
> Etot = -2037.3640 EKtot = 16864.0840 EPtot = -18901.4480
> BOND = 2970.1927 ANGLE = 11913.6344 DIHED = 11187.3323
> 1-4 NB = 3277.6617 1-4 EEL = -47645.6782 VDWAALS = -9107.0392
> EELEC = 8502.4483 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 459.9947 VIRIAL = 1997.9330 VOLUME = 440163.8908
> Density = 0.4799
> ------------------------------------------------------------------------------
>
>
> NSTEP = 139000 TIME(PS) = 278.000 TEMP(K) = 296.67 PRESS = -102.3
> Etot = -1967.1911 EKtot = 16801.8672 EPtot = -18769.0583
> BOND = 2913.4400 ANGLE = 12091.3575 DIHED = 11174.1782
> 1-4 NB = 3268.7765 1-4 EEL = -47686.0629 VDWAALS = -9052.2519
> EELEC = 8521.5043 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 456.4995 VIRIAL = 1426.2504 VOLUME = 438975.0359
> Density = 0.4812
> ------------------------------------------------------------------------------
>
>
> NSTEP = 140000 TIME(PS) = 280.000 TEMP(K) = 300.44 PRESS = -174.8
> Etot = -1612.2857 EKtot = 17015.2793 EPtot = -18627.5650
> BOND = 2959.3406 ANGLE = 12170.5666 DIHED = 11191.1450
> 1-4 NB = 3254.5288 1-4 EEL = -47695.9736 VDWAALS = -9044.2790
> EELEC = 8537.1066 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 464.3324 VIRIAL = 2114.5219 VOLUME = 437163.3799
> Density = 0.4832
> ------------------------------------------------------------------------------
>
>
> NSTEP = 141000 TIME(PS) = 282.000 TEMP(K) = 297.96 PRESS = -208.1
> Etot = -1858.3682 EKtot = 16874.7695 EPtot = -18733.1377
> BOND = 2928.4224 ANGLE = 11976.5792 DIHED = 11212.3601
> 1-4 NB = 3252.0460 1-4 EEL = -47572.4865 VDWAALS = -9059.8806
> EELEC = 8529.8217 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 425.1588 VIRIAL = 2381.4989 VOLUME = 435370.8078
> Density = 0.4852
> ------------------------------------------------------------------------------
>
>
> NSTEP = 142000 TIME(PS) = 284.000 TEMP(K) = 296.94 PRESS = -212.8
> Etot = -1909.5445 EKtot = 16817.0430 EPtot = -18726.5874
> BOND = 2983.9769 ANGLE = 12010.5692 DIHED = 11163.0509
> 1-4 NB = 3252.9352 1-4 EEL = -47447.2789 VDWAALS = -9109.6240
> EELEC = 8419.7833 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 454.1490 VIRIAL = 2444.3172 VOLUME = 433188.0219
> Density = 0.4876
> ------------------------------------------------------------------------------
>
>
> NSTEP = 143000 TIME(PS) = 286.000 TEMP(K) = 299.39 PRESS = -215.7
> Etot = -1826.7768 EKtot = 16956.0664 EPtot = -18782.8432
> BOND = 2938.2812 ANGLE = 12049.7443 DIHED = 11246.8654
> 1-4 NB = 3236.3358 1-4 EEL = -47611.3304 VDWAALS = -9139.4502
> EELEC = 8496.7108 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 447.1248 VIRIAL = 2456.0345 VOLUME = 431433.8613
> Density = 0.4896
> ------------------------------------------------------------------------------
>
>
> NSTEP = 144000 TIME(PS) = 288.000 TEMP(K) = 297.25 PRESS = -65.7
> Etot = -1984.8332 EKtot = 16834.9941 EPtot = -18819.8273
> BOND = 2919.4425 ANGLE = 12000.5014 DIHED = 11199.7438
> 1-4 NB = 3234.6332 1-4 EEL = -47581.9940 VDWAALS = -9018.5205
> EELEC = 8426.3662 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 425.4709 VIRIAL = 1034.5816 VOLUME = 429649.0312
> Density = 0.4916
> ------------------------------------------------------------------------------
>
>
> NSTEP = 145000 TIME(PS) = 290.000 TEMP(K) = 297.12 PRESS = -237.2
> Etot = -1972.1289 EKtot = 16827.6055 EPtot = -18799.7344
> BOND = 2936.1131 ANGLE = 11946.8497 DIHED = 11230.1385
> 1-4 NB = 3258.9700 1-4 EEL = -47609.1316 VDWAALS = -9026.7095
> EELEC = 8464.0354 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 453.1635 VIRIAL = 2642.9667 VOLUME = 427488.0056
> Density = 0.4941
> ------------------------------------------------------------------------------
>
>
> NSTEP = 146000 TIME(PS) = 292.000 TEMP(K) = 297.47 PRESS = -218.5
> Etot = -1955.7990 EKtot = 16846.9844 EPtot = -18802.7834
> BOND = 2915.4177 ANGLE = 12011.5020 DIHED = 11195.8600
> 1-4 NB = 3286.5374 1-4 EEL = -47610.1844 VDWAALS = -9071.3911
> EELEC = 8469.4751 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 427.0172 VIRIAL = 2433.9877 VOLUME = 425488.3089
> Density = 0.4964
> ------------------------------------------------------------------------------
>
>
> NSTEP = 147000 TIME(PS) = 294.000 TEMP(K) = 296.69 PRESS = -272.9
> Etot = -1881.8746 EKtot = 16803.2031 EPtot = -18685.0777
> BOND = 2981.9806 ANGLE = 11982.7674 DIHED = 11230.2446
> 1-4 NB = 3269.3043 1-4 EEL = -47579.0120 VDWAALS = -9061.8198
> EELEC = 8491.4573 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 449.9431 VIRIAL = 2945.9369 VOLUME = 423540.5775
> Density = 0.4987
> ------------------------------------------------------------------------------
>
>
> NSTEP = 148000 TIME(PS) = 296.000 TEMP(K) = 295.47 PRESS = -16.7
> Etot = -2032.0756 EKtot = 16733.7852 EPtot = -18765.8607
> BOND = 2969.6978 ANGLE = 11923.1850 DIHED = 11230.2331
> 1-4 NB = 3214.9544 1-4 EEL = -47538.3397 VDWAALS = -8982.7704
> EELEC = 8417.1789 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 433.9652 VIRIAL = 586.4180 VOLUME = 422115.7014
> Density = 0.5004
> ------------------------------------------------------------------------------
>
>
> NSTEP = 149000 TIME(PS) = 298.000 TEMP(K) = 301.77 PRESS = -197.1
> Etot = -1846.0592 EKtot = 17090.9043 EPtot = -18936.9635
> BOND = 2933.1579 ANGLE = 11816.2879 DIHED = 11185.1557
> 1-4 NB = 3231.1739 1-4 EEL = -47538.3665 VDWAALS = -9020.7088
> EELEC = 8456.3364 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 416.8105 VIRIAL = 2204.0093 VOLUME = 420015.8610
> Density = 0.5029
> ------------------------------------------------------------------------------
>
>
> NSTEP = 150000 TIME(PS) = 300.000 TEMP(K) = 296.27 PRESS = -93.3
> Etot = -1896.1473 EKtot = 16779.4492 EPtot = -18675.5965
> BOND = 2989.0202 ANGLE = 12065.9838 DIHED = 11225.5918
> 1-4 NB = 3263.0266 1-4 EEL = -47609.5688 VDWAALS = -9083.1205
> EELEC = 8473.4703 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 443.2869 VIRIAL = 1284.0618 VOLUME = 417554.9580
> Density = 0.5059
> ------------------------------------------------------------------------------
>
>
> NSTEP = 151000 TIME(PS) = 302.000 TEMP(K) = 296.57 PRESS = -202.5
> Etot = -2169.0401 EKtot = 16795.9883 EPtot = -18965.0283
> BOND = 2842.4078 ANGLE = 11910.0425 DIHED = 11190.5453
> 1-4 NB = 3247.4212 1-4 EEL = -47589.9528 VDWAALS = -9077.7408
> EELEC = 8512.2486 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 433.2917 VIRIAL = 2249.4224 VOLUME = 415432.7796
> Density = 0.5084
> ------------------------------------------------------------------------------
>
>
> NSTEP = 152000 TIME(PS) = 304.000 TEMP(K) = 297.86 PRESS = -238.8
> Etot = -1979.9716 EKtot = 16869.0977 EPtot = -18849.0693
> BOND = 2987.5078 ANGLE = 12013.0651 DIHED = 11175.4389
> 1-4 NB = 3250.3096 1-4 EEL = -47624.2184 VDWAALS = -9119.3023
> EELEC = 8468.1301 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 429.9969 VIRIAL = 2559.4105 VOLUME = 413067.4620
> Density = 0.5114
> ------------------------------------------------------------------------------
>
>
> NSTEP = 153000 TIME(PS) = 306.000 TEMP(K) = 297.87 PRESS = -85.3
> Etot = -1803.0848 EKtot = 16869.8789 EPtot = -18672.9637
> BOND = 2966.8018 ANGLE = 12019.9460 DIHED = 11227.0368
> 1-4 NB = 3267.3826 1-4 EEL = -47521.5855 VDWAALS = -9017.6174
> EELEC = 8385.0719 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 466.9631 VIRIAL = 1222.7335 VOLUME = 410348.9551
> Density = 0.5147
> ------------------------------------------------------------------------------
>
>
> NSTEP = 154000 TIME(PS) = 308.000 TEMP(K) = 299.17 PRESS = -65.6
> Etot = -1892.4766 EKtot = 16943.6270 EPtot = -18836.1035
> BOND = 2937.4545 ANGLE = 12039.5807 DIHED = 11245.3969
> 1-4 NB = 3236.8490 1-4 EEL = -47590.0298 VDWAALS = -9160.1490
> EELEC = 8454.7942 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 437.7150 VIRIAL = 1016.3022 VOLUME = 408690.6939
> Density = 0.5168
> ------------------------------------------------------------------------------
>
>
> NSTEP = 155000 TIME(PS) = 310.000 TEMP(K) = 297.23 PRESS = -67.7
> Etot = -1962.4282 EKtot = 16833.3770 EPtot = -18795.8051
> BOND = 2914.3151 ANGLE = 12042.1716 DIHED = 11259.5959
> 1-4 NB = 3236.3648 1-4 EEL = -47587.6526 VDWAALS = -9089.2821
> EELEC = 8428.6823 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 430.1666 VIRIAL = 1025.4164 VOLUME = 406951.0885
> Density = 0.5190
> ------------------------------------------------------------------------------
>
>
> NSTEP = 156000 TIME(PS) = 312.000 TEMP(K) = 299.35 PRESS = -383.8
> Etot = -1861.1815 EKtot = 16953.8398 EPtot = -18815.0213
> BOND = 2943.4877 ANGLE = 12204.6850 DIHED = 11150.4234
> 1-4 NB = 3252.6186 1-4 EEL = -47659.1356 VDWAALS = -9161.1432
> EELEC = 8454.0427 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 480.3926 VIRIAL = 3836.9868 VOLUME = 405030.5557
> Density = 0.5215
> ------------------------------------------------------------------------------
>
>
> NSTEP = 157000 TIME(PS) = 314.000 TEMP(K) = 300.39 PRESS = -128.8
> Etot = -1814.2317 EKtot = 17012.5801 EPtot = -18826.8117
> BOND = 2936.3542 ANGLE = 11927.0010 DIHED = 11289.6657
> 1-4 NB = 3271.8564 1-4 EEL = -47493.1243 VDWAALS = -9150.8222
> EELEC = 8392.2575 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 452.7813 VIRIAL = 1573.4631 VOLUME = 402879.2515
> Density = 0.5243
> ------------------------------------------------------------------------------
>
>
> NSTEP = 158000 TIME(PS) = 316.000 TEMP(K) = 298.11 PRESS = -260.1
> Etot = -1898.0350 EKtot = 16883.2598 EPtot = -18781.2948
> BOND = 2977.6997 ANGLE = 12048.0891 DIHED = 11268.6086
> 1-4 NB = 3229.8751 1-4 EEL = -47639.3367 VDWAALS = -9179.6111
> EELEC = 8513.3805 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 466.4855 VIRIAL = 2720.0559 VOLUME = 401256.9933
> Density = 0.5264
> ------------------------------------------------------------------------------
>
>
> NSTEP = 159000 TIME(PS) = 318.000 TEMP(K) = 300.73 PRESS = -166.7
> Etot = -1854.1010 EKtot = 17031.7031 EPtot = -18885.8042
> BOND = 2964.2996 ANGLE = 11911.3850 DIHED = 11272.5699
> 1-4 NB = 3248.4662 1-4 EEL = -47612.7926 VDWAALS = -9121.3341
> EELEC = 8451.6018 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 451.3256 VIRIAL = 1887.8859 VOLUME = 399059.0289
> Density = 0.5293
> ------------------------------------------------------------------------------
>
>
> NSTEP = 160000 TIME(PS) = 320.000 TEMP(K) = 296.27 PRESS = -210.7
> Etot = -2053.0081 EKtot = 16779.4590 EPtot = -18832.4671
> BOND = 2947.1267 ANGLE = 11954.8696 DIHED = 11200.9195
> 1-4 NB = 3283.3891 1-4 EEL = -47521.3898 VDWAALS = -9093.7212
> EELEC = 8396.3389 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 460.3724 VIRIAL = 2265.1320 VOLUME = 396774.9045
> Density = 0.5324
> ------------------------------------------------------------------------------
>
>
> NSTEP = 161000 TIME(PS) = 322.000 TEMP(K) = 299.80 PRESS = 29.2
> Etot = -1878.0123 EKtot = 16979.2617 EPtot = -18857.2740
> BOND = 2979.9097 ANGLE = 12014.3690 DIHED = 11192.9003
> 1-4 NB = 3234.7516 1-4 EEL = -47625.7951 VDWAALS = -9043.9694
> EELEC = 8390.5599 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 435.9085 VIRIAL = 186.8940 VOLUME = 394607.6811
> Density = 0.5353
> ------------------------------------------------------------------------------
>
>
> NSTEP = 162000 TIME(PS) = 324.000 TEMP(K) = 300.11 PRESS = -166.3
> Etot = -1811.1578 EKtot = 16996.6875 EPtot = -18807.8453
> BOND = 2916.4802 ANGLE = 12025.8535 DIHED = 11206.1034
> 1-4 NB = 3262.2326 1-4 EEL = -47596.0048 VDWAALS = -9070.0617
> EELEC = 8447.5515 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 429.7606 VIRIAL = 1838.6851 VOLUME = 392405.3315
> Density = 0.5383
> ------------------------------------------------------------------------------
>
>
> NSTEP = 163000 TIME(PS) = 326.000 TEMP(K) = 296.58 PRESS = -98.9
> Etot = -2087.7832 EKtot = 16796.8086 EPtot = -18884.5918
> BOND = 2902.4180 ANGLE = 12061.7438 DIHED = 11228.6919
> 1-4 NB = 3245.1470 1-4 EEL = -47619.5673 VDWAALS = -9128.3876
> EELEC = 8425.3623 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 395.7786 VIRIAL = 1228.5125 VOLUME = 390110.6889
> Density = 0.5414
> ------------------------------------------------------------------------------
>
>
> NSTEP = 164000 TIME(PS) = 328.000 TEMP(K) = 300.69 PRESS = -154.9
> Etot = -1877.7105 EKtot = 17029.4785 EPtot = -18907.1890
> BOND = 2955.4016 ANGLE = 12034.3128 DIHED = 11236.1309
> 1-4 NB = 3258.4725 1-4 EEL = -47689.6473 VDWAALS = -9173.7005
> EELEC = 8471.8411 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 463.1259 VIRIAL = 1761.4756 VOLUME = 388180.4927
> Density = 0.5441
> ------------------------------------------------------------------------------
>
>
> NSTEP = 165000 TIME(PS) = 330.000 TEMP(K) = 296.96 PRESS = -153.2
> Etot = -1894.7474 EKtot = 16818.1973 EPtot = -18712.9447
> BOND = 2963.1993 ANGLE = 12248.7189 DIHED = 11202.9223
> 1-4 NB = 3251.5773 1-4 EEL = -47739.8529 VDWAALS = -9169.4136
> EELEC = 8529.9041 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 436.8864 VIRIAL = 1713.5993 VOLUME = 385945.1589
> Density = 0.5473
> ------------------------------------------------------------------------------
>
>
> NSTEP = 166000 TIME(PS) = 332.000 TEMP(K) = 299.52 PRESS = -172.2
> Etot = -1797.1036 EKtot = 16963.4551 EPtot = -18760.5586
> BOND = 2952.7692 ANGLE = 12088.3955 DIHED = 11296.5976
> 1-4 NB = 3257.2496 1-4 EEL = -47649.3814 VDWAALS = -9200.8337
> EELEC = 8494.6447 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 433.7804 VIRIAL = 1860.5186 VOLUME = 383633.8422
> Density = 0.5506
> ------------------------------------------------------------------------------
>
>
> NSTEP = 167000 TIME(PS) = 334.000 TEMP(K) = 299.22 PRESS = -74.8
> Etot = -1863.6354 EKtot = 16946.2051 EPtot = -18809.8405
> BOND = 2953.1533 ANGLE = 12114.0648 DIHED = 11211.5308
> 1-4 NB = 3280.2675 1-4 EEL = -47628.4385 VDWAALS = -9110.1345
> EELEC = 8369.7162 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 424.7447 VIRIAL = 1040.7267 VOLUME = 381508.0013
> Density = 0.5537
> ------------------------------------------------------------------------------
>
>
> NSTEP = 168000 TIME(PS) = 336.000 TEMP(K) = 301.72 PRESS = -221.7
> Etot = -1854.2286 EKtot = 17087.7773 EPtot = -18942.0059
> BOND = 2883.4927 ANGLE = 12084.0181 DIHED = 11204.0718
> 1-4 NB = 3275.3383 1-4 EEL = -47667.2925 VDWAALS = -9121.7933
> EELEC = 8400.1589 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 457.2240 VIRIAL = 2274.4884 VOLUME = 379639.5394
> Density = 0.5564
> ------------------------------------------------------------------------------
>
>
> NSTEP = 169000 TIME(PS) = 338.000 TEMP(K) = 296.48 PRESS = -350.0
> Etot = -2081.7928 EKtot = 16790.9336 EPtot = -18872.7264
> BOND = 2931.2223 ANGLE = 12127.6772 DIHED = 11200.8400
> 1-4 NB = 3270.8885 1-4 EEL = -47652.1606 VDWAALS = -9191.8153
> EELEC = 8440.6216 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 467.1016 VIRIAL = 3322.2162 VOLUME = 377854.5899
> Density = 0.5590
> ------------------------------------------------------------------------------
>
>
> NSTEP = 170000 TIME(PS) = 340.000 TEMP(K) = 297.49 PRESS = -168.7
> Etot = -2136.3796 EKtot = 16848.3828 EPtot = -18984.7624
> BOND = 2937.2875 ANGLE = 12025.0964 DIHED = 11244.6006
> 1-4 NB = 3240.4482 1-4 EEL = -47655.8502 VDWAALS = -9197.7081
> EELEC = 8421.3633 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 451.2137 VIRIAL = 1819.3762 VOLUME = 375613.8630
> Density = 0.5623
> ------------------------------------------------------------------------------
>
>
> NSTEP = 171000 TIME(PS) = 342.000 TEMP(K) = 298.11 PRESS = -144.4
> Etot = -1919.1352 EKtot = 16883.6484 EPtot = -18802.7837
> BOND = 2861.6881 ANGLE = 12104.7523 DIHED = 11313.9960
> 1-4 NB = 3241.7141 1-4 EEL = -47439.1222 VDWAALS = -9203.4536
> EELEC = 8317.6418 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 476.8353 VIRIAL = 1640.7936 VOLUME = 373218.6173
> Density = 0.5660
> ------------------------------------------------------------------------------
>
>
> NSTEP = 172000 TIME(PS) = 344.000 TEMP(K) = 297.61 PRESS = -92.3
> Etot = -2170.4988 EKtot = 16855.2461 EPtot = -19025.7449
> BOND = 2900.8254 ANGLE = 11976.3556 DIHED = 11283.9427
> 1-4 NB = 3271.0818 1-4 EEL = -47637.2383 VDWAALS = -9206.9539
> EELEC = 8386.2418 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 453.7199 VIRIAL = 1193.6212 VOLUME = 371139.2888
> Density = 0.5691
> ------------------------------------------------------------------------------
>
>
> NSTEP = 173000 TIME(PS) = 346.000 TEMP(K) = 299.04 PRESS = -159.7
> Etot = -1924.6533 EKtot = 16936.0508 EPtot = -18860.7041
> BOND = 2914.1724 ANGLE = 12115.9516 DIHED = 11295.3999
> 1-4 NB = 3243.1471 1-4 EEL = -47583.5417 VDWAALS = -9247.6501
> EELEC = 8401.8167 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 463.3792 VIRIAL = 1737.2074 VOLUME = 369513.0269
> Density = 0.5716
> ------------------------------------------------------------------------------
>
>
> NSTEP = 174000 TIME(PS) = 348.000 TEMP(K) = 296.15 PRESS = -178.0
> Etot = -2225.1388 EKtot = 16772.3945 EPtot = -18997.5333
> BOND = 2917.5258 ANGLE = 11946.1763 DIHED = 11209.5823
> 1-4 NB = 3237.1517 1-4 EEL = -47519.6562 VDWAALS = -9235.5609
> EELEC = 8447.2477 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 405.4899 VIRIAL = 1817.9969 VOLUME = 367495.3944
> Density = 0.5748
> ------------------------------------------------------------------------------
>
>
> NSTEP = 175000 TIME(PS) = 350.000 TEMP(K) = 299.42 PRESS = -65.8
> Etot = -2315.7883 EKtot = 16957.6504 EPtot = -19273.4387
> BOND = 2912.0662 ANGLE = 11831.6709 DIHED = 11232.5397
> 1-4 NB = 3281.6199 1-4 EEL = -47648.8215 VDWAALS = -9277.9241
> EELEC = 8395.4103 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 453.8937 VIRIAL = 973.7078 VOLUME = 365638.0500
> Density = 0.5777
> ------------------------------------------------------------------------------
>
>
> NSTEP = 176000 TIME(PS) = 352.000 TEMP(K) = 293.92 PRESS = 66.3
> Etot = -2242.1516 EKtot = 16646.0957 EPtot = -18888.2473
> BOND = 2896.9835 ANGLE = 12161.3107 DIHED = 11218.5932
> 1-4 NB = 3264.2972 1-4 EEL = -47574.4894 VDWAALS = -9197.2194
> EELEC = 8342.2770 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 445.6299 VIRIAL = -75.7108 VOLUME = 364275.1831
> Density = 0.5798
> ------------------------------------------------------------------------------
>
>
> NSTEP = 177000 TIME(PS) = 354.000 TEMP(K) = 297.67 PRESS = 23.2
> Etot = -2277.0021 EKtot = 16858.7969 EPtot = -19135.7990
> BOND = 2910.2042 ANGLE = 11835.2167 DIHED = 11234.6231
> 1-4 NB = 3282.9486 1-4 EEL = -47581.2807 VDWAALS = -9148.0166
> EELEC = 8330.5056 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 426.5055 VIRIAL = 244.9460 VOLUME = 363116.8795
> Density = 0.5817
> ------------------------------------------------------------------------------
>
>
> NSTEP = 178000 TIME(PS) = 356.000 TEMP(K) = 294.41 PRESS = -157.4
> Etot = -2160.8683 EKtot = 16673.9785 EPtot = -18834.8469
> BOND = 3054.5327 ANGLE = 12134.7511 DIHED = 11242.5780
> 1-4 NB = 3234.7270 1-4 EEL = -47650.2890 VDWAALS = -9263.4639
> EELEC = 8412.3172 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 437.8915 VIRIAL = 1666.5796 VOLUME = 361634.4777
> Density = 0.5841
> ------------------------------------------------------------------------------
>
>
> NSTEP = 179000 TIME(PS) = 358.000 TEMP(K) = 296.94 PRESS = -38.4
> Etot = -1977.9125 EKtot = 16817.2832 EPtot = -18795.1957
> BOND = 3007.0125 ANGLE = 12133.7674 DIHED = 11169.5879
> 1-4 NB = 3263.2654 1-4 EEL = -47669.6744 VDWAALS = -9094.1246
> EELEC = 8394.9702 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 417.2650 VIRIAL = 715.8949 VOLUME = 359819.3725
> Density = 0.5870
> ------------------------------------------------------------------------------
>
>
> NSTEP = 180000 TIME(PS) = 360.000 TEMP(K) = 298.17 PRESS = -165.6
> Etot = -1981.4840 EKtot = 16887.0527 EPtot = -18868.5367
> BOND = 2944.9537 ANGLE = 12139.3614 DIHED = 11245.7877
> 1-4 NB = 3269.6767 1-4 EEL = -47674.1300 VDWAALS = -9236.0737
> EELEC = 8441.8873 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 465.0591 VIRIAL = 1744.8701 VOLUME = 357897.5740
> Density = 0.5902
> ------------------------------------------------------------------------------
>
>
> NSTEP = 181000 TIME(PS) = 362.000 TEMP(K) = 297.33 PRESS = -114.7
> Etot = -2237.2589 EKtot = 16839.5391 EPtot = -19076.7980
> BOND = 2923.4011 ANGLE = 12031.0751 DIHED = 11242.8250
> 1-4 NB = 3278.8936 1-4 EEL = -47577.5574 VDWAALS = -9285.9662
> EELEC = 8310.5308 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 432.5190 VIRIAL = 1315.4274 VOLUME = 356384.5171
> Density = 0.5927
> ------------------------------------------------------------------------------
>
>
> NSTEP = 182000 TIME(PS) = 364.000 TEMP(K) = 295.60 PRESS = -215.4
> Etot = -2310.0217 EKtot = 16741.2949 EPtot = -19051.3166
> BOND = 2887.2341 ANGLE = 11998.0906 DIHED = 11306.0610
> 1-4 NB = 3269.4565 1-4 EEL = -47561.8090 VDWAALS = -9318.3034
> EELEC = 8367.9536 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 448.1271 VIRIAL = 2098.1500 VOLUME = 354758.9401
> Density = 0.5954
> ------------------------------------------------------------------------------
>
>
> NSTEP = 183000 TIME(PS) = 366.000 TEMP(K) = 295.72 PRESS = -133.2
> Etot = -2219.1494 EKtot = 16747.8145 EPtot = -18966.9638
> BOND = 2865.0249 ANGLE = 12195.3745 DIHED = 11178.9543
> 1-4 NB = 3274.2006 1-4 EEL = -47636.5232 VDWAALS = -9235.6659
> EELEC = 8391.6710 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 453.2455 VIRIAL = 1468.7525 VOLUME = 353152.9547
> Density = 0.5981
> ------------------------------------------------------------------------------
>
>
> NSTEP = 184000 TIME(PS) = 368.000 TEMP(K) = 298.67 PRESS = -167.6
> Etot = -1954.4634 EKtot = 16915.1387 EPtot = -18869.6021
> BOND = 3006.6176 ANGLE = 12050.1157 DIHED = 11275.0637
> 1-4 NB = 3275.6526 1-4 EEL = -47601.8323 VDWAALS = -9234.1207
> EELEC = 8358.9013 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 431.0479 VIRIAL = 1702.7206 VOLUME = 351354.5370
> Density = 0.6012
> ------------------------------------------------------------------------------
>
>
> NSTEP = 185000 TIME(PS) = 370.000 TEMP(K) = 295.94 PRESS = -25.0
> Etot = -2347.3514 EKtot = 16760.3086 EPtot = -19107.6600
> BOND = 2950.3015 ANGLE = 12026.3826 DIHED = 11216.8280
> 1-4 NB = 3251.1462 1-4 EEL = -47665.8278 VDWAALS = -9211.3266
> EELEC = 8324.8362 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 447.1446 VIRIAL = 635.7370 VOLUME = 349453.4784
> Density = 0.6044
> ------------------------------------------------------------------------------
>
>
> NSTEP = 186000 TIME(PS) = 372.000 TEMP(K) = 297.30 PRESS = -144.9
> Etot = -2269.4184 EKtot = 16837.8066 EPtot = -19107.2250
> BOND = 2954.5828 ANGLE = 12009.7957 DIHED = 11163.1911
> 1-4 NB = 3268.6167 1-4 EEL = -47657.7399 VDWAALS = -9238.3470
> EELEC = 8392.6756 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 429.6567 VIRIAL = 1518.8313 VOLUME = 348068.7766
> Density = 0.6068
> ------------------------------------------------------------------------------
>
>
> NSTEP = 187000 TIME(PS) = 374.000 TEMP(K) = 297.10 PRESS = 84.9
> Etot = -1963.0999 EKtot = 16826.5234 EPtot = -18789.6233
> BOND = 3006.7205 ANGLE = 12216.8093 DIHED = 11219.1214
> 1-4 NB = 3261.8623 1-4 EEL = -47687.5926 VDWAALS = -9188.2229
> EELEC = 8381.6788 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 456.4238 VIRIAL = -178.9198 VOLUME = 346549.7310
> Density = 0.6095
> ------------------------------------------------------------------------------
>
>
> NSTEP = 188000 TIME(PS) = 376.000 TEMP(K) = 298.58 PRESS = -231.7
> Etot = -2057.8221 EKtot = 16910.1797 EPtot = -18968.0018
> BOND = 2930.4610 ANGLE = 12110.5075 DIHED = 11226.2484
> 1-4 NB = 3244.9635 1-4 EEL = -47607.6881 VDWAALS = -9227.3013
> EELEC = 8354.8072 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 415.4633 VIRIAL = 2141.1774 VOLUME = 345016.0602
> Density = 0.6122
> ------------------------------------------------------------------------------
>
>
> NSTEP = 189000 TIME(PS) = 378.000 TEMP(K) = 296.32 PRESS = -86.5
> Etot = -2443.7547 EKtot = 16781.8359 EPtot = -19225.5906
> BOND = 2910.6587 ANGLE = 11906.4084 DIHED = 11187.4622
> 1-4 NB = 3235.4304 1-4 EEL = -47521.0894 VDWAALS = -9259.6289
> EELEC = 8315.1681 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 415.1342 VIRIAL = 1056.7972 VOLUME = 343577.7395
> Density = 0.6148
> ------------------------------------------------------------------------------
>
>
> NSTEP = 190000 TIME(PS) = 380.000 TEMP(K) = 296.55 PRESS = -84.4
> Etot = -2361.4016 EKtot = 16795.3164 EPtot = -19156.7180
> BOND = 2931.1363 ANGLE = 11984.3514 DIHED = 11175.1119
> 1-4 NB = 3258.3450 1-4 EEL = -47602.1820 VDWAALS = -9264.1432
> EELEC = 8360.6625 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 423.4123 VIRIAL = 1046.6113 VOLUME = 342146.5609
> Density = 0.6173
> ------------------------------------------------------------------------------
>
>
> NSTEP = 191000 TIME(PS) = 382.000 TEMP(K) = 297.97 PRESS = -293.8
> Etot = -2166.2820 EKtot = 16875.4453 EPtot = -19041.7273
> BOND = 2907.5013 ANGLE = 12087.2057 DIHED = 11256.9308
> 1-4 NB = 3268.5665 1-4 EEL = -47656.4873 VDWAALS = -9302.5693
> EELEC = 8397.1249 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 437.7216 VIRIAL = 2599.3709 VOLUME = 340761.0639
> Density = 0.6199
> ------------------------------------------------------------------------------
>
>
> NSTEP = 192000 TIME(PS) = 384.000 TEMP(K) = 296.00 PRESS = -56.8
> Etot = -2258.2020 EKtot = 16763.8945 EPtot = -19022.0966
> BOND = 2922.3066 ANGLE = 12127.7140 DIHED = 11226.8265
> 1-4 NB = 3224.0392 1-4 EEL = -47673.2923 VDWAALS = -9262.1738
> EELEC = 8412.4832 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 453.0074 VIRIAL = 869.2696 VOLUME = 339242.7634
> Density = 0.6226
> ------------------------------------------------------------------------------
>
>
> NSTEP = 193000 TIME(PS) = 386.000 TEMP(K) = 298.65 PRESS = -246.4
> Etot = -2144.5625 EKtot = 16914.0859 EPtot = -19058.6485
> BOND = 2924.6143 ANGLE = 12033.4486 DIHED = 11257.0831
> 1-4 NB = 3265.0599 1-4 EEL = -47648.2860 VDWAALS = -9347.1212
> EELEC = 8456.5528 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 483.8832 VIRIAL = 2280.6806 VOLUME = 337688.1832
> Density = 0.6255
> ------------------------------------------------------------------------------
>
>
> NSTEP = 194000 TIME(PS) = 388.000 TEMP(K) = 298.46 PRESS = -142.2
> Etot = -2122.6673 EKtot = 16903.1094 EPtot = -19025.7767
> BOND = 2929.6886 ANGLE = 12112.2965 DIHED = 11212.6402
> 1-4 NB = 3223.2882 1-4 EEL = -47613.7701 VDWAALS = -9274.8377
> EELEC = 8384.9176 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 444.7098 VIRIAL = 1477.4218 VOLUME = 336425.0760
> Density = 0.6278
> ------------------------------------------------------------------------------
>
>
> NSTEP = 195000 TIME(PS) = 390.000 TEMP(K) = 298.73 PRESS = -200.4
> Etot = -2191.1118 EKtot = 16918.5234 EPtot = -19109.6353
> BOND = 2911.2270 ANGLE = 12026.0627 DIHED = 11182.6566
> 1-4 NB = 3265.6827 1-4 EEL = -47598.6860 VDWAALS = -9269.9911
> EELEC = 8373.4128 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 459.2432 VIRIAL = 1907.0407 VOLUME = 334600.3823
> Density = 0.6313
> ------------------------------------------------------------------------------
>
>
> NSTEP = 196000 TIME(PS) = 392.000 TEMP(K) = 297.61 PRESS = -73.4
> Etot = -2235.4132 EKtot = 16854.9805 EPtot = -19090.3937
> BOND = 2937.7332 ANGLE = 11973.4444 DIHED = 11248.0902
> 1-4 NB = 3264.5129 1-4 EEL = -47638.7517 VDWAALS = -9307.4944
> EELEC = 8432.0717 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 432.9430 VIRIAL = 961.1733 VOLUME = 333212.2353
> Density = 0.6339
> ------------------------------------------------------------------------------
>
>
> NSTEP = 197000 TIME(PS) = 394.000 TEMP(K) = 300.22 PRESS = -76.8
> Etot = -2000.8523 EKtot = 17002.6758 EPtot = -19003.5280
> BOND = 2960.3660 ANGLE = 12066.6222 DIHED = 11222.3239
> 1-4 NB = 3238.3842 1-4 EEL = -47605.5990 VDWAALS = -9245.1677
> EELEC = 8359.5423 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 453.2093 VIRIAL = 1002.8331 VOLUME = 331661.2163
> Density = 0.6369
> ------------------------------------------------------------------------------
>
>
> NSTEP = 198000 TIME(PS) = 396.000 TEMP(K) = 296.42 PRESS = -200.5
> Etot = -2241.5817 EKtot = 16787.7168 EPtot = -19029.2985
> BOND = 2931.1922 ANGLE = 12034.9659 DIHED = 11260.0347
> 1-4 NB = 3288.7680 1-4 EEL = -47614.2844 VDWAALS = -9364.1811
> EELEC = 8434.2062 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 471.2030 VIRIAL = 1900.6972 VOLUME = 330131.0197
> Density = 0.6398
> ------------------------------------------------------------------------------
>
>
> NSTEP = 199000 TIME(PS) = 398.000 TEMP(K) = 296.17 PRESS = -179.2
> Etot = -2459.6795 EKtot = 16773.6836 EPtot = -19233.3631
> BOND = 2886.7429 ANGLE = 12050.7329 DIHED = 11253.6486
> 1-4 NB = 3248.6328 1-4 EEL = -47773.8329 VDWAALS = -9370.6536
> EELEC = 8471.3661 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 436.5704 VIRIAL = 1710.8307 VOLUME = 329247.9315
> Density = 0.6415
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 969701.15695 834511.15563 -494420.66053
> wrapping first mol.: 969701.15695 834511.15563 -494420.66053
>
> NSTEP = 200000 TIME(PS) = 400.000 TEMP(K) =********* PRESS = 72193.9
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1646698.1151 DIHED = 31917.2318
> 1-4 NB = 0.0000 1-4 EEL = -0.0432 VDWAALS = **************
> EELEC = 762183.7278 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -137856.7452 VOLUME = 8160841.1910
> Density = 0.0259
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 1307150.06481 1302025.99556 -591573.79452
> wrapping first mol.: 1259941.81270 927416.22433 -560399.94992
> wrapping first mol.: 1259941.81270 927416.22433 -560399.94992
>
> NSTEP = 201000 TIME(PS) = 402.000 TEMP(K) =********* PRESS = 7637.4
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1731005.8043 DIHED = 32134.0685
> 1-4 NB = 0.0000 1-4 EEL = -0.0205 VDWAALS = **************
> EELEC = 2485702.7999 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 8359428.8229 VOLUME = 25612343.3643
> Density = 0.0082
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 1190113.46187 598793.09588 -589695.85948
> wrapping first mol.: 1087847.59876 517322.63545 -586625.66780
> wrapping first mol.: 1087847.59876 517322.63545 -586625.66780
>
> NSTEP = 202000 TIME(PS) = 404.000 TEMP(K) =********* PRESS = 9937.2
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1764895.8479 DIHED = 32222.3530
> 1-4 NB = 0.0000 1-4 EEL = -0.0167 VDWAALS = **************
> EELEC = 4091502.2361 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 3385296.5972 VOLUME = 42867963.7078
> Density = 0.0049
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 1496389.87594 468528.93653 -622224.29062
> wrapping first mol.: 912052.64306 120563.18200 -1063148.05947
> wrapping first mol.: 912052.64306 120563.18200 -1063148.05947
>
> NSTEP = 203000 TIME(PS) = 406.000 TEMP(K) =********* PRESS = 7081.0
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1788488.2215 DIHED = 32094.2266
> 1-4 NB = 0.0000 1-4 EEL = -0.0150 VDWAALS = **************
> EELEC = 5429019.6900 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 3414979.1022 VOLUME = 59965373.2667
> Density = 0.0035
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 944524.51566 19234.25140 -1198252.93841
> wrapping first mol.: 1234321.59182 7243.17123 -989758.04549
> wrapping first mol.: 1234321.59182 7243.17123 -989758.04549
>
> NSTEP = 204000 TIME(PS) = 408.000 TEMP(K) =********* PRESS = 7672.7
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1804732.2901 DIHED = 31982.3193
> 1-4 NB = 0.0000 1-4 EEL = -0.0142 VDWAALS = **************
> EELEC = 7032057.3067 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -227522.4245 VOLUME = 77328652.0366
> Density = 0.0027
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 1379333.87777 -93162.43541 -1398319.58735
> wrapping first mol.: 1355605.60308 141256.38217 -1576147.82556
> wrapping first mol.: 1355605.60308 141256.38217 -1576147.82556
>
> NSTEP = 205000 TIME(PS) = 410.000 TEMP(K) =********* PRESS = 7043.6
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1827428.4697 DIHED = 32358.4211
> 1-4 NB = 0.0000 1-4 EEL = -0.0137 VDWAALS = **************
> EELEC = 8218593.9654 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -1802353.7860 VOLUME = 94590653.1618
> Density = 0.0022
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 1505488.69933 571306.43813 -1822359.56683
> wrapping first mol.: 1451731.38584 852512.24951 -1733972.28338
> wrapping first mol.: 1451731.38584 852512.24951 -1733972.28338
>
> NSTEP = 206000 TIME(PS) = 412.000 TEMP(K) =********* PRESS = 4456.8
> Etot = ************** EKtot = ************** EPtot = 46092258.4471
> BOND = -0.0000 ANGLE = 1830834.5663 DIHED = 32192.2762
> 1-4 NB = 0.0000 1-4 EEL = -0.0128 VDWAALS = 34638540.7203
> EELEC = 9590690.8971 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 1777704.4685 VOLUME = 112288350.3771
> Density = 0.0019
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 942267.47799 1045204.26130 -1659855.63087
> wrapping first mol.: 694658.66323 1219579.43282 -1632017.18036
> wrapping first mol.: 694658.66323 1219579.43282 -1632017.18036
>
> NSTEP = 207000 TIME(PS) = 414.000 TEMP(K) =********* PRESS = 7206.7
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1834367.7256 DIHED = 31815.6618
> 1-4 NB = 0.0000 1-4 EEL = -0.0123 VDWAALS = **************
> EELEC = 11001139.9206 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -7652923.2197 VOLUME = 130049584.0423
> Density = 0.0016
> ------------------------------------------------------------------------------
>
> wrapping first mol.: 477209.28016 1284475.35886 -1803654.18482
> wrapping first mol.: 67237.42374 1497753.32104 -1889001.00724
> wrapping first mol.: 67237.42374 1497753.32104 -1889001.00724
>
> NSTEP = 208000 TIME(PS) = 416.000 TEMP(K) =********* PRESS = 3319.3
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1842630.2842 DIHED = 31912.7778
> 1-4 NB = 0.0000 1-4 EEL = -0.0116 VDWAALS = **************
> EELEC = 12282198.0577 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 1948692.2844 VOLUME = 148381304.1957
> Density = 0.0014
> ------------------------------------------------------------------------------
>
> wrapping first mol.: -355099.42302 2179166.36801 -2051265.81595
> wrapping first mol.: -815707.21317 2433929.60910 -2126115.56640
> wrapping first mol.: -815707.21317 2433929.60910 -2126115.56640
>
> NSTEP = 209000 TIME(PS) = 418.000 TEMP(K) =********* PRESS = 1786.6
> Etot = ************** EKtot = ************** EPtot = 205799276.5000
> BOND = -0.0000 ANGLE = 1861880.6388 DIHED = 31770.4677
> 1-4 NB = 0.0000 1-4 EEL = -0.0114 VDWAALS = 190288136.6267
> EELEC = 13617488.7783 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 6176916.8385 VOLUME = 166065014.7043
> Density = 0.0013
> ------------------------------------------------------------------------------
>
> wrapping first mol.: -1091905.51553 2268320.37645 -2026545.29562
> wrapping first mol.: -1166827.01815 1965392.04570 -1861231.38993
> wrapping first mol.: -1166827.01815 1965392.04570 -1861231.38993
>
> NSTEP = 210000 TIME(PS) = 420.000 TEMP(K) =********* PRESS = 4843.0
> Etot = ************** EKtot = ************** EPtot = 876918185.3325
> BOND = -0.0000 ANGLE = 1885865.5318 DIHED = 31645.0919
> 1-4 NB = 0.0000 1-4 EEL = -0.0109 VDWAALS = 860666720.2572
> EELEC = 14333954.4625 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -6696325.3606 VOLUME = 184372152.6830
> Density = 0.0011
> ------------------------------------------------------------------------------
>
> wrapping first mol.: -1168656.51498 2207719.43622 -1678352.74750
> wrapping first mol.:-16679526.48888 -7357196.48272 -3486318.56986
> wrapping first mol.:-16679526.48888 -7357196.48272 -3486318.56986
>
> NSTEP = 211000 TIME(PS) = 422.000 TEMP(K) =********* PRESS = 2000.3
> Etot = ************** EKtot = ************** EPtot = 658315587.1845
> BOND = -0.0000 ANGLE = 1918261.0241 DIHED = 31323.0468
> 1-4 NB = 0.0000 1-4 EEL = -0.0106 VDWAALS = 640487445.5696
> EELEC = 15878557.5544 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 3802920.2149 VOLUME = 203297033.2064
> Density = 0.0010
> ------------------------------------------------------------------------------
>
> wrapping first mol.:152714801.77042100779952.09377 19223038.33916
> wrapping first mol.: -1104195.97259 2491705.38551 -1496476.12075
> wrapping first mol.: -1104195.97259 2491705.38551 -1496476.12075
>
> NSTEP = 212000 TIME(PS) = 424.000 TEMP(K) =********* PRESS = 1973.6
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1934469.0783 DIHED = 30934.7616
> 1-4 NB = 0.0000 1-4 EEL = -0.0103 VDWAALS = **************
> EELEC = ************** EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 3129554.4090 VOLUME = 221839308.2029
> Density = 0.0010
> ------------------------------------------------------------------------------
>
> wrapping first mol.:*********************************************
> wrapping first mol.: -1625252.35542 2633729.52470 -1185675.68546
> wrapping first mol.: -1625252.35542 2633729.52470 -1185675.68546
>
> NSTEP = 213000 TIME(PS) = 426.000 TEMP(K) =********* PRESS = 2029.6
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1959816.6743 DIHED = 30692.2135
> 1-4 NB = 0.0000 1-4 EEL = -0.0109 VDWAALS = **************
> EELEC = ************** EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 2051217.9646 VOLUME = 240336354.0931
> Density = 0.0009
> ------------------------------------------------------------------------------
>
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
>
> NSTEP = 214000 TIME(PS) = 428.000 TEMP(K) = Infinity PRESS = 2129.3
> Etot = Infinity EKtot = Infinity EPtot = **************
> BOND = -0.0000 ANGLE = 1980356.9159 DIHED = 30490.9459
> 1-4 NB = 0.0000 1-4 EEL = -0.0095 VDWAALS = **************
> EELEC = ************** EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 679791.6474 VOLUME = 258909423.4955
> Density = 0.0008
> ------------------------------------------------------------------------------
>
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
>
> NSTEP = 215000 TIME(PS) = 430.000 TEMP(K) =********* PRESS = 2177.2
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 1997684.8754 DIHED = 29746.3739
> 1-4 NB = 0.0000 1-4 EEL = -0.0092 VDWAALS = 94992381.6223
> EELEC = ************** EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -462074.0179 VOLUME = 277505926.1985
> Density = 0.0008
> ------------------------------------------------------------------------------
>
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
>
> NSTEP = 216000 TIME(PS) = 432.000 TEMP(K) =********* PRESS = 3356.2
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 2022817.4577 DIHED = 29007.6867
> 1-4 NB = 0.0000 1-4 EEL = -0.0088 VDWAALS = **************
> EELEC = 21177680.5800 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -8869107.1618 VOLUME = 296034786.6735
> Density = 0.0007
> ------------------------------------------------------------------------------
>
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
>
> NSTEP = 217000 TIME(PS) = 434.000 TEMP(K) =********* PRESS = 1308.1
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 2038360.2431 DIHED = 28364.5654
> 1-4 NB = 0.0000 1-4 EEL = -0.0084 VDWAALS = 569494461.2948
> EELEC = ************** EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 3697676.3391 VOLUME = 314596733.4211
> Density = 0.0007
> ------------------------------------------------------------------------------
>
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
>
> NSTEP = 218000 TIME(PS) = 436.000 TEMP(K) =********* PRESS = 1314.0
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 2056682.4457 DIHED = 28358.0336
> 1-4 NB = 0.0000 1-4 EEL = -0.0081 VDWAALS = 22818355.2668
> EELEC = ************** EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 3127965.8836 VOLUME = 333257986.3368
> Density = 0.0006
> ------------------------------------------------------------------------------
>
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
>
> NSTEP = 219000 TIME(PS) = 438.000 TEMP(K) =********* PRESS = 1293.9
> Etot = ************** EKtot = ************** EPtot = **************
> BOND = -0.0000 ANGLE = 2074758.3080 DIHED = 27538.8408
> 1-4 NB = 0.0000 1-4 EEL = -0.0083 VDWAALS = **************
> EELEC = ************** EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = 2750375.4684 VOLUME = 351955186.9209
> Density = 0.0006
> ------------------------------------------------------------------------------
>
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
>
> NSTEP = 220000 TIME(PS) = 440.000 TEMP(K) = Infinity PRESS = 2059.2
> Etot = Infinity EKtot = Infinity EPtot = **************
> BOND = -0.0000 ANGLE = 2086972.5533 DIHED = 26120.3673
> 1-4 NB = 0.0000 1-4 EEL = -0.0080 VDWAALS = **************
> EELEC = 35513248.8668 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -3885260.8916 VOLUME = 370395078.8170
> Density = 0.0006
> ------------------------------------------------------------------------------
>
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
> wrapping first mol.:*********************************************
>
> NSTEP = 221000 TIME(PS) = 442.000 TEMP(K) = Infinity PRESS = 1854.6
> Etot = Infinity EKtot = Infinity EPtot = **************
> BOND = -0.0000 ANGLE = 2116826.5216 DIHED = 23857.0986
> 1-4 NB = 0.0000 1-4 EEL = -0.0077 VDWAALS = **************
> EELEC = ************** EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 12582912.0000 VIRIAL = -2859702.5784 VOLUME = 385644051.8555
> Density = 0.0005
> ------------------------------------------------------------------------------
>
> -------------- next part --------------
> nitial MD of cys
> &cntrl
> iwrap = 1,
> imin = 0,
> irest = 0,
> ntx = 1,
> nstlim = 5000000,
> dt = 0.002,
> ntwx = 1000,
> ntpr = 1000,
> ntb =2,
> ntc=2,
> ntf=2,
> cut = 8,
> ntt = 3,
> ntp=1,
> pres0=1,
> taup=3,
> gamma_ln = 2.0,
> temp0 = 298.15,
> &end
>
> ------------------------------
>
> Message: 4
> Date: Wed, 12 Jun 2013 15:33:36 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Protein leaving periodic box
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOauAqzWst8Jh+mh1cYbEC96UYGA1TY7Jt74QPD3x+mDUg.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> I suspect that the protein doesn't actually break apart - this is a
> visual artifact caused by 'wrapping' the coordinates. You can use the
> 'autoimage' command in cpptraj to re-image your solute back into the
> primary cell.
>
> -Dan
>
> On Wed, Jun 12, 2013 at 2:56 PM, Hailin Huang <hailin.huang.my.liu.edu> wrote:
> > Dear Amber users,
> >
> > I am running a prodution simulation of protein 3TNP in a 10A solvatebox.
> > After about 25 ns of simlutation time, part of the protein drifts out of
> > the solvent box. As the protein falls out further it breaks apart
> > eventually and the fragment comes back in from the other side of the
> > solvent box. Will I solve this problem by simply increasing the size of the
> > solvent box? Is there a way to lock the protein within the box? Thanks for
> > any help!
> >
> > The input file follows
> >
> > &cntrl
> > imin=0, irest=0, ntx=1,
> > ntpr=2000, ntwx=2000, nstlim=2500000,
> > dt=0.001, ntt=3, tempi=300,
> > temp0=300, gamma_ln=1.0, ig=-1,
> > ntp=0, ntc=2, ntf=2, cut=8,
> > ntb=1, iwrap=1, ioutfm=1,
> > /
> >
> > Regards,
> > Richard
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 12 Jun 2013 16:38:29 -0600
> From: Jason Slingsby <jason.slingsby.gmail.com>
> Subject: [AMBER] bad atom type: N3 (In MMGBSA decomp calculations)
> To: amber.ambermd.org
> Message-ID:
> <CANRfLwbF=P8AxuMG6hHOo0Wps1HF31OS5zEUwDdnwZ1LrE3LiA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Amber Users,
>
> I am trying to run a decomposition analysis on a protein and keep running
> into the following error:
>
> bad atom type: N3
> CalcError: /amber12/bin/sander failed with prmtop complex.prmtop!
>
> I have successfully run a different system through the decomp which also
> contained N3 atom types. Looking through the .prmtops I see no differences
> in the way that the amino acids containing type N3 were written between the
> two different systems.
>
> Any ideas as to what could be causing this error? The protein that isn't
> working is a channel made of 5 subunits. I noticed that all subunits begin
> with N3 (on SER and THR residues) Could this have something to do with it
> or is it some other issue?
>
> Thanks,
> Jason
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 13 Jun 2013 09:22:20 +0800
> From: "#YIP YEW MUN#" <YIPY0005.e.ntu.edu.sg>
> Subject: [AMBER] Step by step tutorial to using Ptraj in generating
> DCCM
> To: amber.ambermd.org
> Message-ID:
> <CAFqeT9ecQf90-eDDA9ckFkpLkxrw_QZRQtuWp2VUn2=bQa-cCQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> I wish to ask the steps to using ptraj in generating DCCM for alpha-C in
> proteins. I tried searching the net for a tutorial or some sort but to no
> avail. I would appreciate if there is someone to list out the step-by-step
> way to generating DCCM.
>
> Many thanks.
>
> --
> Regards
> Yip Yew Mun
> Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 13 Jun 2013 09:40:42 +0800
> From: Dongshan Wei <dswei0523.gmail.com>
> Subject: [AMBER] Unknown redidue when using tleap
> To: AMBER Mailing List <AMBER.ambermd.org>
> Cc: zhangmk.cigit.ac.cn
> Message-ID:
> <CANBrWcqaKTnQkuDetxBz4=XmU9q9KWQ=vFSJfgEc-C2VEQbWxA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi All.
>
> I'm an beginner of Amber software. Now I'm using Amber to do a simulation
> about 2TRX protein. I donwloaded the 2TRX.pdb file from the PDB database.
> When I used tleap to create the .prmtop and .inpcrd files, I got error
> information as follows. The error information indicates that tleap cannot
> read the CU and MPD residues. How can I solve the problem?
>
> Thank you in advance!
>
> Dongshan Wei
>
>
> =========================================================
>
> tleap -s -f ~/Amber12/amber12/dat/leap/cmd/oldff/leaprc.ff03
> > m = loadpdb 2TRX.pdb
> Loading PDB file: ./2TRX.pdb
> (starting new molecule for chain B)
> (starting new molecule for chain A)
> (starting new molecule for chain B)
> -- residue 5: duplicate [ C] atoms (total 2)
> -- residue 5: duplicate [ O] atoms (total 2)
> -- residue 6: duplicate [ C] atoms (total 2)
> -- residue 6: duplicate [ CA] atoms (total 2)
> -- residue 6: duplicate [ CB] atoms (total 2)
> -- residue 6: duplicate [ CD2] atoms (total 2)
> -- residue 6: duplicate [ CE1] atoms (total 2)
> -- residue 6: duplicate [ CG] atoms (total 2)
> -- residue 6: duplicate [ N] atoms (total 2)
> -- residue 6: duplicate [ ND1] atoms (total 2)
> -- residue 6: duplicate [ NE2] atoms (total 2)
> -- residue 6: duplicate [ O] atoms (total 2)
> -- residue 7: duplicate [ N] atoms (total 2)
> -- residue 23: duplicate [ CD1] atoms (total 2)
> -- residue 23: duplicate [ CG1] atoms (total 2)
> -- residue 23: duplicate [ CG2] atoms (total 2)
> -- residue 47: duplicate [ CG] atoms (total 2)
> -- residue 47: duplicate [ OD1] atoms (total 2)
> -- residue 47: duplicate [ OD2] atoms (total 2)
> -- residue 48: duplicate [ CD] atoms (total 2)
> -- residue 48: duplicate [ CG] atoms (total 2)
> -- residue 48: duplicate [ OE1] atoms (total 2)
> -- residue 48: duplicate [ OE2] atoms (total 2)
> -- residue 58: duplicate [ CD1] atoms (total 2)
> -- residue 58: duplicate [ CD2] atoms (total 2)
> -- residue 80: duplicate [ CD1] atoms (total 2)
> -- residue 80: duplicate [ CD2] atoms (total 2)
> -- residue 114: duplicate [ C] atoms (total 2)
> -- residue 114: duplicate [ CA] atoms (total 2)
> -- residue 114: duplicate [ CB] atoms (total 2)
> -- residue 114: duplicate [ CD2] atoms (total 2)
> -- residue 114: duplicate [ CE1] atoms (total 2)
> -- residue 114: duplicate [ CG] atoms (total 2)
> -- residue 114: duplicate [ N] atoms (total 2)
> -- residue 114: duplicate [ ND1] atoms (total 2)
> -- residue 114: duplicate [ NE2] atoms (total 2)
> -- residue 114: duplicate [ O] atoms (total 2)
> -- residue 155: duplicate [ CG] atoms (total 2)
> -- residue 155: duplicate [ OD1] atoms (total 2)
> -- residue 155: duplicate [ OD2] atoms (total 2)
> -- residue 166: duplicate [ CD1] atoms (total 2)
> -- residue 166: duplicate [ CD2] atoms (total 2)
> -- residue 188: duplicate [ CD1] atoms (total 2)
> -- residue 188: duplicate [ CD2] atoms (total 2)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Unknown residue: CU number: 216 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: MPD number: 217 type: Nonterminal
> Unknown residue: MPD number: 218 type: Nonterminal
> Unknown residue: MPD number: 219 type: Nonterminal
> Unknown residue: MPD number: 220 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: CU number: 221 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: MPD number: 222 type: Nonterminal
> Unknown residue: MPD number: 223 type: Nonterminal
> Unknown residue: MPD number: 224 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: CU sequence: 217
> Created a new atom named: CU within residue: .R<CU 217>
> Creating new UNIT for residue: MPD sequence: 218
> Created a new atom named: C1 within residue: .R<MPD 218>
> Created a new atom named: C2 within residue: .R<MPD 218>
> Created a new atom named: O2 within residue: .R<MPD 218>
> Created a new atom named: CM within residue: .R<MPD 218>
> Created a new atom named: C3 within residue: .R<MPD 218>
> Created a new atom named: C4 within residue: .R<MPD 218>
> Created a new atom named: O4 within residue: .R<MPD 218>
> Created a new atom named: C5 within residue: .R<MPD 218>
> Creating new UNIT for residue: MPD sequence: 219
> Created a new atom named: C1 within residue: .R<MPD 219>
> Created a new atom named: C2 within residue: .R<MPD 219>
> Created a new atom named: O2 within residue: .R<MPD 219>
> Created a new atom named: CM within residue: .R<MPD 219>
> Created a new atom named: C3 within residue: .R<MPD 219>
> Created a new atom named: C4 within residue: .R<MPD 219>
> Created a new atom named: O4 within residue: .R<MPD 219>
> Created a new atom named: C5 within residue: .R<MPD 219>
> Creating new UNIT for residue: MPD sequence: 220
> Created a new atom named: C1 within residue: .R<MPD 220>
> Created a new atom named: C2 within residue: .R<MPD 220>
> Created a new atom named: O2 within residue: .R<MPD 220>
> Created a new atom named: CM within residue: .R<MPD 220>
> Created a new atom named: C3 within residue: .R<MPD 220>
> Created a new atom named: C4 within residue: .R<MPD 220>
> Created a new atom named: O4 within residue: .R<MPD 220>
> Created a new atom named: C5 within residue: .R<MPD 220>
> Creating new UNIT for residue: MPD sequence: 221
> Created a new atom named: C1 within residue: .R<MPD 221>
> Created a new atom named: C2 within residue: .R<MPD 221>
> Created a new atom named: O2 within residue: .R<MPD 221>
> Created a new atom named: CM within residue: .R<MPD 221>
> Created a new atom named: C3 within residue: .R<MPD 221>
> Created a new atom named: C4 within residue: .R<MPD 221>
> Created a new atom named: O4 within residue: .R<MPD 221>
> Created a new atom named: C5 within residue: .R<MPD 221>
> Creating new UNIT for residue: CU sequence: 222
> Created a new atom named: CU within residue: .R<CU 222>
> Creating new UNIT for residue: MPD sequence: 223
> Created a new atom named: C1 within residue: .R<MPD 223>
> Created a new atom named: C2 within residue: .R<MPD 223>
> Created a new atom named: O2 within residue: .R<MPD 223>
> Created a new atom named: CM within residue: .R<MPD 223>
> Created a new atom named: C3 within residue: .R<MPD 223>
> Created a new atom named: C4 within residue: .R<MPD 223>
> Created a new atom named: O4 within residue: .R<MPD 223>
> Created a new atom named: C5 within residue: .R<MPD 223>
> Creating new UNIT for residue: MPD sequence: 224
> Created a new atom named: C1 within residue: .R<MPD 224>
> Created a new atom named: C2 within residue: .R<MPD 224>
> Created a new atom named: O2 within residue: .R<MPD 224>
> Created a new atom named: CM within residue: .R<MPD 224>
> Created a new atom named: C3 within residue: .R<MPD 224>
> Created a new atom named: C4 within residue: .R<MPD 224>
> Created a new atom named: O4 within residue: .R<MPD 224>
> Created a new atom named: C5 within residue: .R<MPD 224>
> Creating new UNIT for residue: MPD sequence: 225
> Created a new atom named: C1 within residue: .R<MPD 225>
> Created a new atom named: C2 within residue: .R<MPD 225>
> Created a new atom named: O2 within residue: .R<MPD 225>
> Created a new atom named: CM within residue: .R<MPD 225>
> Created a new atom named: C3 within residue: .R<MPD 225>
> Created a new atom named: C4 within residue: .R<MPD 225>
> Created a new atom named: O4 within residue: .R<MPD 225>
> Created a new atom named: C5 within residue: .R<MPD 225>
> total atoms in file: 1886
> Leap added 1946 missing atoms according to residue templates:
> 1946 H / lone pairs
> The file contained 58 atoms not in residue templates
> >
>
> =================================================================
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 12 Jun 2013 21:43:14 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] csh problem
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20130613014314.GB10330.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Wed, Jun 12, 2013, Albert wrote:
>
> > Error: /bin/csh not found on your system! Install csh or tcsh and rerun
> > configure.
> >
> >
> > Actually, I've installed csh at /home/albert/bin/csh,
>
> There is no easy way to avoid putting csh in /bin, which is where shells
> "always" reside. Unfortunately, there are tons of files that refer to
> /bin/csh...of course, we all should have read Tom Christiansen and avoided
> this, but we didn't.
>
> A link should work, but one way or another you need privileges to modify /bin.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 13 Jun 2013 03:49:33 +0200
> From: Xioling Chuang <xioling_c.hotmail.com>
> Subject: Re: [AMBER] parameters of ions for TIP5P water box
> To: amber mailing list <amber.ambermd.org>
> Message-ID: <DUB118-W28E24CED5FB626A0D5AE4A81870.phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Prof. David Case,
> Thank you very much for your reply.
> Best Regards,
> Xioling
>
>
> > Date: Wed, 12 Jun 2013 07:58:32 -0400
> > From: case.biomaps.rutgers.edu
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] parameters of ions for TIP5P water box
> >
> > On Wed, Jun 12, 2013, Xioling Chuang wrote:
> > >
> > > Thank you very much for your message. I will try to use TIP4PEW. By the
> > > way, for water, do I need to load "frcmod.tip4pew" into tleap?
> >
> > Yes...please see Section 2.10 in the AmberTools manual.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> Message: 10
> Date: Thu, 13 Jun 2013 03:56:29 +0100
> From: ET <sketchfoot.gmail.com>
> Subject: Re: [AMBER] Unknown redidue when using tleap
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAP_EkXut3HohubVT4f0SgyCJ2Ar7v88tSyNB_OX6he5hNucCpA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi, I believe you have to make a library file that defines the unknown
> residues and load them before loading the pdb using the loadoff command.
> though there may be a better way of doing it for your specific residues.
> Someone else may have a better idea.. the following link could help:
>
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/section2.htm
>
> br,
> g
>
>
> On 13 June 2013 02:40, Dongshan Wei <dswei0523.gmail.com> wrote:
>
> > Hi All.
> >
> > I'm an beginner of Amber software. Now I'm using Amber to do a simulation
> > about 2TRX protein. I donwloaded the 2TRX.pdb file from the PDB database.
> > When I used tleap to create the .prmtop and .inpcrd files, I got error
> > information as follows. The error information indicates that tleap cannot
> > read the CU and MPD residues. How can I solve the problem?
> >
> > Thank you in advance!
> >
> > Dongshan Wei
> >
> >
> > =========================================================
> >
> > tleap -s -f ~/Amber12/amber12/dat/leap/cmd/oldff/leaprc.ff03
> > > m = loadpdb 2TRX.pdb
> > Loading PDB file: ./2TRX.pdb
> > (starting new molecule for chain B)
> > (starting new molecule for chain A)
> > (starting new molecule for chain B)
> > -- residue 5: duplicate [ C] atoms (total 2)
> > -- residue 5: duplicate [ O] atoms (total 2)
> > -- residue 6: duplicate [ C] atoms (total 2)
> > -- residue 6: duplicate [ CA] atoms (total 2)
> > -- residue 6: duplicate [ CB] atoms (total 2)
> > -- residue 6: duplicate [ CD2] atoms (total 2)
> > -- residue 6: duplicate [ CE1] atoms (total 2)
> > -- residue 6: duplicate [ CG] atoms (total 2)
> > -- residue 6: duplicate [ N] atoms (total 2)
> > -- residue 6: duplicate [ ND1] atoms (total 2)
> > -- residue 6: duplicate [ NE2] atoms (total 2)
> > -- residue 6: duplicate [ O] atoms (total 2)
> > -- residue 7: duplicate [ N] atoms (total 2)
> > -- residue 23: duplicate [ CD1] atoms (total 2)
> > -- residue 23: duplicate [ CG1] atoms (total 2)
> > -- residue 23: duplicate [ CG2] atoms (total 2)
> > -- residue 47: duplicate [ CG] atoms (total 2)
> > -- residue 47: duplicate [ OD1] atoms (total 2)
> > -- residue 47: duplicate [ OD2] atoms (total 2)
> > -- residue 48: duplicate [ CD] atoms (total 2)
> > -- residue 48: duplicate [ CG] atoms (total 2)
> > -- residue 48: duplicate [ OE1] atoms (total 2)
> > -- residue 48: duplicate [ OE2] atoms (total 2)
> > -- residue 58: duplicate [ CD1] atoms (total 2)
> > -- residue 58: duplicate [ CD2] atoms (total 2)
> > -- residue 80: duplicate [ CD1] atoms (total 2)
> > -- residue 80: duplicate [ CD2] atoms (total 2)
> > -- residue 114: duplicate [ C] atoms (total 2)
> > -- residue 114: duplicate [ CA] atoms (total 2)
> > -- residue 114: duplicate [ CB] atoms (total 2)
> > -- residue 114: duplicate [ CD2] atoms (total 2)
> > -- residue 114: duplicate [ CE1] atoms (total 2)
> > -- residue 114: duplicate [ CG] atoms (total 2)
> > -- residue 114: duplicate [ N] atoms (total 2)
> > -- residue 114: duplicate [ ND1] atoms (total 2)
> > -- residue 114: duplicate [ NE2] atoms (total 2)
> > -- residue 114: duplicate [ O] atoms (total 2)
> > -- residue 155: duplicate [ CG] atoms (total 2)
> > -- residue 155: duplicate [ OD1] atoms (total 2)
> > -- residue 155: duplicate [ OD2] atoms (total 2)
> > -- residue 166: duplicate [ CD1] atoms (total 2)
> > -- residue 166: duplicate [ CD2] atoms (total 2)
> > -- residue 188: duplicate [ CD1] atoms (total 2)
> > -- residue 188: duplicate [ CD2] atoms (total 2)
> >
> > Warning: Atom names in each residue should be unique.
> > (Same-name atoms are handled by using the first
> > occurrence and by ignoring the rest.
> > Frequently duplicate atom names stem from alternate
> > conformations in the PDB file.)
> >
> > Unknown residue: CU number: 216 type: Terminal/beginning
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: MPD number: 217 type: Nonterminal
> > Unknown residue: MPD number: 218 type: Nonterminal
> > Unknown residue: MPD number: 219 type: Nonterminal
> > Unknown residue: MPD number: 220 type: Terminal/last
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: CU number: 221 type: Terminal/beginning
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: MPD number: 222 type: Nonterminal
> > Unknown residue: MPD number: 223 type: Nonterminal
> > Unknown residue: MPD number: 224 type: Terminal/last
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Creating new UNIT for residue: CU sequence: 217
> > Created a new atom named: CU within residue: .R<CU 217>
> > Creating new UNIT for residue: MPD sequence: 218
> > Created a new atom named: C1 within residue: .R<MPD 218>
> > Created a new atom named: C2 within residue: .R<MPD 218>
> > Created a new atom named: O2 within residue: .R<MPD 218>
> > Created a new atom named: CM within residue: .R<MPD 218>
> > Created a new atom named: C3 within residue: .R<MPD 218>
> > Created a new atom named: C4 within residue: .R<MPD 218>
> > Created a new atom named: O4 within residue: .R<MPD 218>
> > Created a new atom named: C5 within residue: .R<MPD 218>
> > Creating new UNIT for residue: MPD sequence: 219
> > Created a new atom named: C1 within residue: .R<MPD 219>
> > Created a new atom named: C2 within residue: .R<MPD 219>
> > Created a new atom named: O2 within residue: .R<MPD 219>
> > Created a new atom named: CM within residue: .R<MPD 219>
> > Created a new atom named: C3 within residue: .R<MPD 219>
> > Created a new atom named: C4 within residue: .R<MPD 219>
> > Created a new atom named: O4 within residue: .R<MPD 219>
> > Created a new atom named: C5 within residue: .R<MPD 219>
> > Creating new UNIT for residue: MPD sequence: 220
> > Created a new atom named: C1 within residue: .R<MPD 220>
> > Created a new atom named: C2 within residue: .R<MPD 220>
> > Created a new atom named: O2 within residue: .R<MPD 220>
> > Created a new atom named: CM within residue: .R<MPD 220>
> > Created a new atom named: C3 within residue: .R<MPD 220>
> > Created a new atom named: C4 within residue: .R<MPD 220>
> > Created a new atom named: O4 within residue: .R<MPD 220>
> > Created a new atom named: C5 within residue: .R<MPD 220>
> > Creating new UNIT for residue: MPD sequence: 221
> > Created a new atom named: C1 within residue: .R<MPD 221>
> > Created a new atom named: C2 within residue: .R<MPD 221>
> > Created a new atom named: O2 within residue: .R<MPD 221>
> > Created a new atom named: CM within residue: .R<MPD 221>
> > Created a new atom named: C3 within residue: .R<MPD 221>
> > Created a new atom named: C4 within residue: .R<MPD 221>
> > Created a new atom named: O4 within residue: .R<MPD 221>
> > Created a new atom named: C5 within residue: .R<MPD 221>
> > Creating new UNIT for residue: CU sequence: 222
> > Created a new atom named: CU within residue: .R<CU 222>
> > Creating new UNIT for residue: MPD sequence: 223
> > Created a new atom named: C1 within residue: .R<MPD 223>
> > Created a new atom named: C2 within residue: .R<MPD 223>
> > Created a new atom named: O2 within residue: .R<MPD 223>
> > Created a new atom named: CM within residue: .R<MPD 223>
> > Created a new atom named: C3 within residue: .R<MPD 223>
> > Created a new atom named: C4 within residue: .R<MPD 223>
> > Created a new atom named: O4 within residue: .R<MPD 223>
> > Created a new atom named: C5 within residue: .R<MPD 223>
> > Creating new UNIT for residue: MPD sequence: 224
> > Created a new atom named: C1 within residue: .R<MPD 224>
> > Created a new atom named: C2 within residue: .R<MPD 224>
> > Created a new atom named: O2 within residue: .R<MPD 224>
> > Created a new atom named: CM within residue: .R<MPD 224>
> > Created a new atom named: C3 within residue: .R<MPD 224>
> > Created a new atom named: C4 within residue: .R<MPD 224>
> > Created a new atom named: O4 within residue: .R<MPD 224>
> > Created a new atom named: C5 within residue: .R<MPD 224>
> > Creating new UNIT for residue: MPD sequence: 225
> > Created a new atom named: C1 within residue: .R<MPD 225>
> > Created a new atom named: C2 within residue: .R<MPD 225>
> > Created a new atom named: O2 within residue: .R<MPD 225>
> > Created a new atom named: CM within residue: .R<MPD 225>
> > Created a new atom named: C3 within residue: .R<MPD 225>
> > Created a new atom named: C4 within residue: .R<MPD 225>
> > Created a new atom named: O4 within residue: .R<MPD 225>
> > Created a new atom named: C5 within residue: .R<MPD 225>
> > total atoms in file: 1886
> > Leap added 1946 missing atoms according to residue templates:
> > 1946 H / lone pairs
> > The file contained 58 atoms not in residue templates
> > >
> >
> > =================================================================
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 11
> Date: Thu, 13 Jun 2013 04:11:08 +0100
> From: ET <sketchfoot.gmail.com>
> Subject: Re: [AMBER] Running MD NPT Ensemble Error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAP_EkXvAaWhcMxgbynQMQy=gofXcfSe+aNxP0Nm-DwJ79Ur3Ag.mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> When I've encountered the issue with the ***, i've only usually noticed it
> in my restart files and the problem has been solved by turning iwrap on.
> Are you writing netcdf trajectories (ioutfm & ntxo)? I understand the
> greater level of precision eliminates the typical error associated with
> ****'s in the restart file.
>
> br,
> g
>
>
> On 12 June 2013 22:07, Benjamin Grant <bdgrant15.gmail.com> wrote:
>
> > Hello,
> >
> > I?m modeling a carboxylic acid (palmitoleic and linoleic acids) and having
> > issues with my MD simulations. I used the RESP methodology along with
> > antechamber to get the necessary .prep and .frcmod files. I was able to
> > successfully create a box (~25,000 atoms) for each carboxylic acid using
> > packmol and tleap. I was also able successfully minimize the structure
> > prior to starting my NPT simulations. The simulations seem to start out
> > fine but they crash with the energy, temperature and the VDW contributions
> > to the energy increasing. I also noticed that when ?wrapping first mol?
> > appears for the first time in the md.out file, then my mdcrd and rst-crd
> > file turn to ?****?. I have tried turning iwrap off and the problem still
> > occurs. Also I?m unable to use VMD to see what is happening since the mdcrd
> > file is filled with ?******?. I have attached my input and output files.
> >
> > I?m using Amber 12 with all of the bug fixes.
> >
> > Thanks,
> >
> > Ben
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> ------------------------------
>
> Message: 12
> Date: Thu, 13 Jun 2013 04:24:13 +0100
> From: ET <sketchfoot.gmail.com>
> Subject: Re: [AMBER] Running MD NPT Ensemble Error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAP_EkXty5NTixPfzm4qnDt4q18vW960b94f=x9TPK66JorOjfg.mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> so to clarify, try with ioutfm=1 and ntxo=2, iwrap=0
>
>
> On 13 June 2013 04:11, ET <sketchfoot.gmail.com> wrote:
>
> > When I've encountered the issue with the ***, i've only usually noticed
> > it in my restart files and the problem has been solved by turning iwrap on.
> > Are you writing netcdf trajectories (ioutfm & ntxo)? I understand the
> > greater level of precision eliminates the typical error associated with
> > ****'s in the restart file.
> >
> > br,
> > g
> >
> >
> > On 12 June 2013 22:07, Benjamin Grant <bdgrant15.gmail.com> wrote:
> >
> >> Hello,
> >>
> >> I?m modeling a carboxylic acid (palmitoleic and linoleic acids) and having
> >> issues with my MD simulations. I used the RESP methodology along with
> >> antechamber to get the necessary .prep and .frcmod files. I was able to
> >> successfully create a box (~25,000 atoms) for each carboxylic acid using
> >> packmol and tleap. I was also able successfully minimize the structure
> >> prior to starting my NPT simulations. The simulations seem to start out
> >> fine but they crash with the energy, temperature and the VDW contributions
> >> to the energy increasing. I also noticed that when ?wrapping first mol?
> >> appears for the first time in the md.out file, then my mdcrd and rst-crd
> >> file turn to ?****?. I have tried turning iwrap off and the problem still
> >> occurs. Also I?m unable to use VMD to see what is happening since the
> >> mdcrd
> >> file is filled with ?******?. I have attached my input and output files.
> >>
> >> I?m using Amber 12 with all of the bug fixes.
> >>
> >> Thanks,
> >>
> >> Ben
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
>
>
> ------------------------------
>
> Message: 13
> Date: Thu, 13 Jun 2013 09:37:22 +0200
> From: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] Unknown redidue when using tleap
> To: AMBER Mailing List <AMBER.ambermd.org>
> Cc: zhangmk.cigit.ac.cn
> Message-ID: <20130613093722.07msl8eehwwowgos.webmail.u-picardie.fr>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Dongshan Wei,
>
> the recognition between the PDB file and the FF loaded is based on the
> atom and residue names; and in a residue two atoms cannot bear the
> same name (so that they can be differentiated).
>
> Observed errors:
> -1 duplicate [ CD1] atoms (total 2)
>
> -> See:
>
> > Warning: Atom names in each residue should be unique.
> > (Same-name atoms are handled by using the first
> > occurrence and by ignoring the rest.
> > Frequently duplicate atom names stem from alternate
> > conformations in the PDB file.)
>
> -2 Unknown residue: MPD number: 217 type: Nonterminal
>
> it looks like you have an unknown residue: check if this residue in
> present in the set of FF libraries you loaded in LEaP; if not you will
> have to develop a new library for this new residue/the corresponding
> molecular fragment. For that you could use R.E.D. or R.E.D. Server;
> See tutorials at:
> http://q4md-forcefieldtools.org/Tutorial/
>
> regards, Francois
>
>
>
> > I'm an beginner of Amber software. Now I'm using Amber to do a simulation
> > about 2TRX protein. I donwloaded the 2TRX.pdb file from the PDB database.
> > When I used tleap to create the .prmtop and .inpcrd files, I got error
> > information as follows. The error information indicates that tleap cannot
> > read the CU and MPD residues. How can I solve the problem?
> >
> > Thank you in advance!
> >
> > Dongshan Wei
> >
> >
> > =========================================================
> >
> > tleap -s -f ~/Amber12/amber12/dat/leap/cmd/oldff/leaprc.ff03
> >> m = loadpdb 2TRX.pdb
> > Loading PDB file: ./2TRX.pdb
> > (starting new molecule for chain B)
> > (starting new molecule for chain A)
> > (starting new molecule for chain B)
> > -- residue 5: duplicate [ C] atoms (total 2)
> > -- residue 5: duplicate [ O] atoms (total 2)
> > -- residue 6: duplicate [ C] atoms (total 2)
> > -- residue 6: duplicate [ CA] atoms (total 2)
> > -- residue 6: duplicate [ CB] atoms (total 2)
> > -- residue 6: duplicate [ CD2] atoms (total 2)
> > -- residue 6: duplicate [ CE1] atoms (total 2)
> > -- residue 6: duplicate [ CG] atoms (total 2)
> > -- residue 6: duplicate [ N] atoms (total 2)
> > -- residue 6: duplicate [ ND1] atoms (total 2)
> > -- residue 6: duplicate [ NE2] atoms (total 2)
> > -- residue 6: duplicate [ O] atoms (total 2)
> > -- residue 7: duplicate [ N] atoms (total 2)
> > -- residue 23: duplicate [ CD1] atoms (total 2)
> > -- residue 23: duplicate [ CG1] atoms (total 2)
> > -- residue 23: duplicate [ CG2] atoms (total 2)
> > -- residue 47: duplicate [ CG] atoms (total 2)
> > -- residue 47: duplicate [ OD1] atoms (total 2)
> > -- residue 47: duplicate [ OD2] atoms (total 2)
> > -- residue 48: duplicate [ CD] atoms (total 2)
> > -- residue 48: duplicate [ CG] atoms (total 2)
> > -- residue 48: duplicate [ OE1] atoms (total 2)
> > -- residue 48: duplicate [ OE2] atoms (total 2)
> > -- residue 58: duplicate [ CD1] atoms (total 2)
> > -- residue 58: duplicate [ CD2] atoms (total 2)
> > -- residue 80: duplicate [ CD1] atoms (total 2)
> > -- residue 80: duplicate [ CD2] atoms (total 2)
> > -- residue 114: duplicate [ C] atoms (total 2)
> > -- residue 114: duplicate [ CA] atoms (total 2)
> > -- residue 114: duplicate [ CB] atoms (total 2)
> > -- residue 114: duplicate [ CD2] atoms (total 2)
> > -- residue 114: duplicate [ CE1] atoms (total 2)
> > -- residue 114: duplicate [ CG] atoms (total 2)
> > -- residue 114: duplicate [ N] atoms (total 2)
> > -- residue 114: duplicate [ ND1] atoms (total 2)
> > -- residue 114: duplicate [ NE2] atoms (total 2)
> > -- residue 114: duplicate [ O] atoms (total 2)
> > -- residue 155: duplicate [ CG] atoms (total 2)
> > -- residue 155: duplicate [ OD1] atoms (total 2)
> > -- residue 155: duplicate [ OD2] atoms (total 2)
> > -- residue 166: duplicate [ CD1] atoms (total 2)
> > -- residue 166: duplicate [ CD2] atoms (total 2)
> > -- residue 188: duplicate [ CD1] atoms (total 2)
> > -- residue 188: duplicate [ CD2] atoms (total 2)
> >
> > Warning: Atom names in each residue should be unique.
> > (Same-name atoms are handled by using the first
> > occurrence and by ignoring the rest.
> > Frequently duplicate atom names stem from alternate
> > conformations in the PDB file.)
> >
> > Unknown residue: CU number: 216 type: Terminal/beginning
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: MPD number: 217 type: Nonterminal
> > Unknown residue: MPD number: 218 type: Nonterminal
> > Unknown residue: MPD number: 219 type: Nonterminal
> > Unknown residue: MPD number: 220 type: Terminal/last
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: CU number: 221 type: Terminal/beginning
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: MPD number: 222 type: Nonterminal
> > Unknown residue: MPD number: 223 type: Nonterminal
> > Unknown residue: MPD number: 224 type: Terminal/last
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Creating new UNIT for residue: CU sequence: 217
> > Created a new atom named: CU within residue: .R<CU 217>
> > Creating new UNIT for residue: MPD sequence: 218
> > Created a new atom named: C1 within residue: .R<MPD 218>
> > Created a new atom named: C2 within residue: .R<MPD 218>
> > Created a new atom named: O2 within residue: .R<MPD 218>
> > Created a new atom named: CM within residue: .R<MPD 218>
> > Created a new atom named: C3 within residue: .R<MPD 218>
> > Created a new atom named: C4 within residue: .R<MPD 218>
> > Created a new atom named: O4 within residue: .R<MPD 218>
> > Created a new atom named: C5 within residue: .R<MPD 218>
> > Creating new UNIT for residue: MPD sequence: 219
> > Created a new atom named: C1 within residue: .R<MPD 219>
> > Created a new atom named: C2 within residue: .R<MPD 219>
> > Created a new atom named: O2 within residue: .R<MPD 219>
> > Created a new atom named: CM within residue: .R<MPD 219>
> > Created a new atom named: C3 within residue: .R<MPD 219>
> > Created a new atom named: C4 within residue: .R<MPD 219>
> > Created a new atom named: O4 within residue: .R<MPD 219>
> > Created a new atom named: C5 within residue: .R<MPD 219>
> > Creating new UNIT for residue: MPD sequence: 220
> > Created a new atom named: C1 within residue: .R<MPD 220>
> > Created a new atom named: C2 within residue: .R<MPD 220>
> > Created a new atom named: O2 within residue: .R<MPD 220>
> > Created a new atom named: CM within residue: .R<MPD 220>
> > Created a new atom named: C3 within residue: .R<MPD 220>
> > Created a new atom named: C4 within residue: .R<MPD 220>
> > Created a new atom named: O4 within residue: .R<MPD 220>
> > Created a new atom named: C5 within residue: .R<MPD 220>
> > Creating new UNIT for residue: MPD sequence: 221
> > Created a new atom named: C1 within residue: .R<MPD 221>
> > Created a new atom named: C2 within residue: .R<MPD 221>
> > Created a new atom named: O2 within residue: .R<MPD 221>
> > Created a new atom named: CM within residue: .R<MPD 221>
> > Created a new atom named: C3 within residue: .R<MPD 221>
> > Created a new atom named: C4 within residue: .R<MPD 221>
> > Created a new atom named: O4 within residue: .R<MPD 221>
> > Created a new atom named: C5 within residue: .R<MPD 221>
> > Creating new UNIT for residue: CU sequence: 222
> > Created a new atom named: CU within residue: .R<CU 222>
> > Creating new UNIT for residue: MPD sequence: 223
> > Created a new atom named: C1 within residue: .R<MPD 223>
> > Created a new atom named: C2 within residue: .R<MPD 223>
> > Created a new atom named: O2 within residue: .R<MPD 223>
> > Created a new atom named: CM within residue: .R<MPD 223>
> > Created a new atom named: C3 within residue: .R<MPD 223>
> > Created a new atom named: C4 within residue: .R<MPD 223>
> > Created a new atom named: O4 within residue: .R<MPD 223>
> > Created a new atom named: C5 within residue: .R<MPD 223>
> > Creating new UNIT for residue: MPD sequence: 224
> > Created a new atom named: C1 within residue: .R<MPD 224>
> > Created a new atom named: C2 within residue: .R<MPD 224>
> > Created a new atom named: O2 within residue: .R<MPD 224>
> > Created a new atom named: CM within residue: .R<MPD 224>
> > Created a new atom named: C3 within residue: .R<MPD 224>
> > Created a new atom named: C4 within residue: .R<MPD 224>
> > Created a new atom named: O4 within residue: .R<MPD 224>
> > Created a new atom named: C5 within residue: .R<MPD 224>
> > Creating new UNIT for residue: MPD sequence: 225
> > Created a new atom named: C1 within residue: .R<MPD 225>
> > Created a new atom named: C2 within residue: .R<MPD 225>
> > Created a new atom named: O2 within residue: .R<MPD 225>
> > Created a new atom named: CM within residue: .R<MPD 225>
> > Created a new atom named: C3 within residue: .R<MPD 225>
> > Created a new atom named: C4 within residue: .R<MPD 225>
> > Created a new atom named: O4 within residue: .R<MPD 225>
> > Created a new atom named: C5 within residue: .R<MPD 225>
> > total atoms in file: 1886
> > Leap added 1946 missing atoms according to residue templates:
> > 1946 H / lone pairs
> > The file contained 58 atoms not in residue templates
>
>
>
>
>
> ------------------------------
>
> Message: 14
> Date: Thu, 13 Jun 2013 10:36:43 +0200
> From: Frank Thommen <structures-it.embl-heidelberg.de>
> Subject: [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2
> To: amber.ambermd.org
> Message-ID: <51B9849B.7030400.embl-heidelberg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
>
> when doing `make install` (after `./configure -mpi gnu`) on our cluster
> (LSF running on CentOS 6.2), I'm getting the following error (only the
> lines for the last compilation block are shown):
>
> amber-12 > make install
> [...]
> make[2]: Entering directory
> `/g/software/linux/pack/amber-12/AmberTools/src/nab'
> mpicc -DCC='"mpicc"' -DCPP='"ucpp -l"' -DFLIBS='"-lsff_mpi -lpbsa
> -larpack -llapack -lblas -L/g/software/linux/pack/amber-12/lib -lnetcdf
> -lgfortran -w "' \
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI \
> -o /g/software/linux/pack/amber-12/bin/mpinab nab.c
> /g/software/linux/pack/amber-12/bin/mpinab -c allatom_to_dna3.nab
> /g/software/linux/pack/amber-12/bin/mpinab -c dna3.nab
> /g/software/linux/pack/amber-12/bin/mpinab -c dna3_to_allatom.nab
> /g/software/linux/pack/amber-12/bin/mpinab -c fd_helix.nab
> mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c
> -o select_atoms.o select_atoms.c
> In file included from select_atoms.c:5:
> /usr/include/string.h:548: error: expected declaration specifiers or
> '...' before '__locale_t'
> /usr/include/string.h:549: error: nonnull argument with out-of-range
> operand number (argument 1, operand 3)
> /usr/include/string.h:552: error: expected declaration specifiers or
> '...' before '__locale_t'
> /usr/include/string.h:553: error: nonnull argument with out-of-range
> operand number (argument 1, operand 4)
> make[2]: *** [select_atoms.o] Error 1
> make[2]: Leaving directory
> `/g/software/linux/pack/amber-12/AmberTools/src/nab'
> make[1]: *** [parallel] Error 2
> make[1]: Leaving directory `/g/software/linux/pack/amber-12/AmberTools/src'
> make: *** [install] Error 2
> amber-12 >
>
>
> The full output of `make install` is posted on http://pastebin.com/QqT9d6pj.
>
>
> This is on CentOS 6.2 (kernel 2.6.32-220.el6.x86_64) on an LSF 7.0.6
> cluster using the MPI implementation which comes with LSF.
>
> Any idea what's going wrong here? The compilation of the serial part
> went fine w/o errors.
>
> Cheers
> frank
>
>
>
> ------------------------------
>
> Message: 15
> Date: Thu, 13 Jun 2013 09:26:22 +0000
> From: Rasha Alqus <rasha.alqus.manchester.ac.uk>
> Subject: [AMBER] glycame06_carbohydrate_hydrogen bond pattern
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <91194318CCF0994BA21082AE31EB74ECE3B314.MBXP14.ds.man.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Amber users
>
> my system is formed from chains of carbohydarate, the chains are connected togather by hydrogen bond, a recent paper have published two type of hydrogen bond pattern present for the system. I have built my system but i would like to know how i can set the hydrogen bond between the chains.
>
> Am using Amber12 and GLYCAM06 force field
>
> Thank you
> Regards
> Rasha
>
>
> ------------------------------
>
> Message: 16
> Date: Thu, 13 Jun 2013 12:57:55 +0200 (CEST)
> From: "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>
> Subject: Re: [AMBER] glycame06_carbohydrate_hydrogen bond pattern
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <1853601853.4127011.1371121075041.JavaMail.root.scai.fraunhofer.de>
> Content-Type: text/plain; charset=utf-8
>
> Hi Rasha,
>
> It will be difficult to specifically set the orientation of hydrogen bonds using Amber programs. One possible way, which I haven't verified, would be to use leap's "impose" command. Another way would be to specify week NMR constraints in the sander input file. An third option, that would be partially outside of Amber, would be to construct the glycans using leap (to get the right atom and residue naming); then open it in a separate external program that can modify internal coordinates and preserve atom and residue names.
>
> Then if you perform Anber MM maximization, the artificial structure you created will be largely conformationally preserved and the internal coordinates will be minimized. However, if you perform unrestrained MD simulations at room or biological temperatures, then all of the intermolecular hydrogen bonds will change and adopt a distribution of conformations and populations. But at least you will have a reasonable input structure.
>
> Cheers,
> Karl
>
> ----- Original Message -----
> From: "Rasha Alqus" <rasha.alqus.manchester.ac.uk>
> To: amber.ambermd.org
> Sent: Thursday, June 13, 2013 11:26:22 AM
> Subject: [AMBER] glycame06_carbohydrate_hydrogen bond pattern
>
> Dear Amber users
>
> my system is formed from chains of carbohydarate, the chains are connected togather by hydrogen bond, a recent paper have published two type of hydrogen bond pattern present for the system. I have built my system but i would like to know how i can set the hydrogen bond between the chains.
>
> Am using Amber12 and GLYCAM06 force field
>
> Thank you
> Regards
> Rasha
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 17
> Date: Thu, 13 Jun 2013 07:47:37 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20130613114737.GA58497.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Thu, Jun 13, 2013, Frank Thommen wrote:
>
> > In file included from select_atoms.c:5:
> > /usr/include/string.h:548: error: expected declaration specifiers or
> > '...' before '__locale_t'
>
> Pretty odd...your compiler doesn't like <string.h>.
>
> What does "mpicc -show" report? How about "gcc --version".
>
> > This is on CentOS 6.2 (kernel 2.6.32-220.el6.x86_64) on an LSF 7.0.6
> > cluster using the MPI implementation which comes with LSF.
>
> By far the safest way to build parallel Amber is to also build your own
> MPI. That way, you know the options are correct, and that the same compiler
> is used for MPI as for Amber. The "implementation that comes with LSF" could
> have all kinds of weird behavior (and apparently does).
>
> Go to $AMBERHOME/AmberTools/src and run "./configure_mpich --help". You
> download the mpich code, re-run this script telling which compiler you want,
> and it will generate an MPI installation that should be compatible and have
> all the correct features enabled.
>
> ...good luck...dac
>
>
>
>
> ------------------------------
>
> Message: 18
> Date: Thu, 13 Jun 2013 14:03:03 +0200
> From: Frank Thommen <structures-it.embl-heidelberg.de>
> Subject: Re: [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <51B9B4F7.4040501.embl-heidelberg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 13.06.13 13:47, David A Case wrote:
> > On Thu, Jun 13, 2013, Frank Thommen wrote:
> >
> >> In file included from select_atoms.c:5:
> >> /usr/include/string.h:548: error: expected declaration specifiers or
> >> '...' before '__locale_t'
> >
> > Pretty odd...your compiler doesn't like <string.h>.
> >
> > What does "mpicc -show" report? How about "gcc --version".
>
> amber-12 > gcc --version
> gcc (GCC) 4.4.4
> Copyright (C) 2010 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions. There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> amber-12 > mpicc -show
> /g/software/linux/pack/gcc-4.4/bin/gcc
> -L/opt/platform_mpi/lib/linux_amd64 -lpcmpio -lpcmpi -ldl
> -I/opt/platform_mpi/include
> amber-12 > which mpicc
> /opt/platform_mpi/bin/mpicc
> amber-12 > which gcc
> /g/software/linux/pack/gcc-4.4/bin/gcc
> amber-12 >
>
>
> I should probably also have told (sorry for the omission), that I built
> the serial binaries under CentOS 5.9 and the gcc I'm using
> (/g/software/linux/pack/gcc-4.4/bin/gcc) has also been built under
> CentOS 5.x.
>
> When trying to build the serial (!) Amber[Tools]12 binaries on the
> cluster (CentOS 6.2), I get even other compilation errors:
>
> [...]
> make[5]: Entering directory
> `/g/software/linux/pack/amber-12/SRC/amber12/AmberTools/src/mtkpp/src/Diagnostics'
> /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I.
> -I../..
> -I/g/software/linux/pack/amber-12/SRC/amber12/AmberTools/src/boost-1.38.0
> -I./.. -DNDEBUG -DUSE_TINYXML -DTIXML_USE_STL -DC99_OK -O2 -fPIC
> -DHAVE_ZLIB -MT MTKException.lo -MD -MP -MF .deps/MTKException.Tpo -c -o
> MTKException.lo MTKException.cpp
> libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../..
> -I/g/software/linux/pack/amber-12/SRC/amber12/AmberTools/src/boost-1.38.0 -I./..
> -DNDEBUG -DUSE_TINYXML -DTIXML_USE_STL -DC99_OK -O2 -fPIC -DHAVE_ZLIB
> -MT MTKException.lo -MD -MP -MF .deps/MTKException.Tpo -c
> MTKException.cpp -o MTKException.o
> In file included from
> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/bits/localefwd.h:42,
> from
> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/string:45,
> from MTKException.h:11,
> from MTKException.cpp:8:
> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/x86_64-unknown-linux-gnu/bits/c++locale.h:52:
> error: 'uselocale' was not declared in this scope
> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/x86_64-unknown-linux-gnu/bits/c++locale.h:52:
> error: invalid type in declaration before ';' token
> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/x86_64-unknown-linux-gnu/bits/c++locale.h:
> In function 'int std::__convert_from_v(__locale_struct* const&, char*,
> int, const char*, ...)':
> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/x86_64-unknown-linux-gnu/bits/c++locale.h:72:
> error: '__gnu_cxx::__uselocale' cannot be used as a function
> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/x86_64-unknown-linux-gnu/bits/c++locale.h:97:
> error: '__gnu_cxx::__uselocale' cannot be used as a function
> make[5]: *** [MTKException.lo] Error 1
> [...]
>
>
> I'll try to completely rebuild with the default gcc on the cluster.
> Unfortunately I'll then probably loose compatibility with CentOS 5.x,
> which is still the most used version in our unit.
>
>
> >> This is on CentOS 6.2 (kernel 2.6.32-220.el6.x86_64) on an LSF 7.0.6
> >> cluster using the MPI implementation which comes with LSF.
> >
> > By far the safest way to build parallel Amber is to also build your own
> > MPI. That way, you know the options are correct, and that the same compiler
> > is used for MPI as for Amber. The "implementation that comes with LSF" could
> > have all kinds of weird behavior (and apparently does).
>
> I'm not sure this is an option for us, as we are required to use an MPI
> build which is integrated into the LSF batch system, so that it can
> handle those jobs correctly. I'm not sure I want - better: I'm sure I
> don't want :-) - to go through the hassles of integrating our own MPI
> build into the cluster setup.
>
> Cheers
> frank
>
>
> >
> > Go to $AMBERHOME/AmberTools/src and run "./configure_mpich --help". You
> > download the mpich code, re-run this script telling which compiler you want,
> > and it will generate an MPI installation that should be compatible and have
> > all the correct features enabled.
> >
> > ...good luck...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Frank Thommen - Structures IT Management and Support - EMBL Heidelberg
> structures-it.embl-heidelberg.de - +49 6221 387 8353
>
>
>
> ------------------------------
>
> Message: 19
> Date: Thu, 13 Jun 2013 08:35:37 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20130613123536.GB58879.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Thu, Jun 13, 2013, Frank Thommen wrote:
> >
> > When trying to build the serial (!) Amber[Tools]12 binaries on the
> > cluster (CentOS 6.2), I get even other compilation errors:
> >
> > [...]
> > In file included from
> > /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/bits/localefwd.h:42,
> > from
> > /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/string:45,
> > from MTKException.h:11,
> > from MTKException.cpp:8:
> > /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/x86_64-unknown-linux-gnu/bits/c++locale.h:52:
> > error: 'uselocale' was not declared in this scope
>
> Again, it seems to be the string library that causes problems. You could of
> course google the error message (add CentOS 6.2 to the search string) to see
> if this is a known problem. It doesn't seem(?) to be related to Amber code.
>
> A workaround is to try adding the -nomtkpp flag to configure, but I'm guessing
> you will get similar errors elsewhere.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 20
> Date: Thu, 13 Jun 2013 15:27:21 +0200
> From: Frank Thommen <structures-it.embl-heidelberg.de>
> Subject: Re: [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <51B9C8B9.4050309.embl-heidelberg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 13.06.13 14:35, David A Case wrote:
> > On Thu, Jun 13, 2013, Frank Thommen wrote:
> >>
> >> When trying to build the serial (!) Amber[Tools]12 binaries on the
> >> cluster (CentOS 6.2), I get even other compilation errors:
> >>
> >> [...]
> >> In file included from
> >> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/bits/localefwd.h:42,
> >> from
> >> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/string:45,
> >> from MTKException.h:11,
> >> from MTKException.cpp:8:
> >> /g/software/linux/pack/gcc-4.4/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.4/../../../../include/c++/4.4.4/x86_64-unknown-linux-gnu/bits/c++locale.h:52:
> >> error: 'uselocale' was not declared in this scope
> >
> > Again, it seems to be the string library that causes problems. You could of
> > course google the error message (add CentOS 6.2 to the search string) to see
> > if this is a known problem. It doesn't seem(?) to be related to Amber code.
> >
> > A workaround is to try adding the -nomtkpp flag to configure, but I'm guessing
> > you will get similar errors elsewhere.
> >
> > ....dac
>
>
> Hi David,
>
> thanks. I could solve the problem by using the gcc (4.4.6) compiler
> provided by LSF which is probably the same that has been used to compile
> the LSF provided MPI build. Now compilation and installation seem to
> work fine and I'll proceed to testing.
>
> Lesson learned: For MPI binaries always use the compiler that was used
> to compile MPI itself.
>
> Thanks for help and pointers.
>
> frank
>
>
>
> ------------------------------
>
> Message: 21
> Date: Thu, 13 Jun 2013 21:49:46 +0800
> From: Dongshan Wei <dswei0523.gmail.com>
> Subject: Re: [AMBER] Unknown redidue when using tleap
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CANBrWcp5fS2BJq-KRXm1jC9=9P3Yba0-36yPCdQE1y15B02spw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi ET and Francois,
>
> Thanks a lot to you. I will take your advice to set up the unknown residue
> libraries first and then use LEaP to create the .prmtop and .inpcrd files.
>
> Dongshan
>
>
> On Thu, Jun 13, 2013 at 3:37 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
> > Dear Dongshan Wei,
> >
> > the recognition between the PDB file and the FF loaded is based on the
> > atom and residue names; and in a residue two atoms cannot bear the
> > same name (so that they can be differentiated).
> >
> > Observed errors:
> > -1 duplicate [ CD1] atoms (total 2)
> >
> > -> See:
> >
> > > Warning: Atom names in each residue should be unique.
> > > (Same-name atoms are handled by using the first
> > > occurrence and by ignoring the rest.
> > > Frequently duplicate atom names stem from alternate
> > > conformations in the PDB file.)
> >
> > -2 Unknown residue: MPD number: 217 type: Nonterminal
> >
> > it looks like you have an unknown residue: check if this residue in
> > present in the set of FF libraries you loaded in LEaP; if not you will
> > have to develop a new library for this new residue/the corresponding
> > molecular fragment. For that you could use R.E.D. or R.E.D. Server;
> > See tutorials at:
> > http://q4md-forcefieldtools.org/Tutorial/
> >
> > regards, Francois
> >
> >
> >
> > > I'm an beginner of Amber software. Now I'm using Amber to do a simulation
> > > about 2TRX protein. I donwloaded the 2TRX.pdb file from the PDB database.
> > > When I used tleap to create the .prmtop and .inpcrd files, I got error
> > > information as follows. The error information indicates that tleap cannot
> > > read the CU and MPD residues. How can I solve the problem?
> > >
> > > Thank you in advance!
> > >
> > > Dongshan Wei
> > >
> > >
> > > =========================================================
> > >
> > > tleap -s -f ~/Amber12/amber12/dat/leap/cmd/oldff/leaprc.ff03
> > >> m = loadpdb 2TRX.pdb
> > > Loading PDB file: ./2TRX.pdb
> > > (starting new molecule for chain B)
> > > (starting new molecule for chain A)
> > > (starting new molecule for chain B)
> > > -- residue 5: duplicate [ C] atoms (total 2)
> > > -- residue 5: duplicate [ O] atoms (total 2)
> > > -- residue 6: duplicate [ C] atoms (total 2)
> > > -- residue 6: duplicate [ CA] atoms (total 2)
> > > -- residue 6: duplicate [ CB] atoms (total 2)
> > > -- residue 6: duplicate [ CD2] atoms (total 2)
> > > -- residue 6: duplicate [ CE1] atoms (total 2)
> > > -- residue 6: duplicate [ CG] atoms (total 2)
> > > -- residue 6: duplicate [ N] atoms (total 2)
> > > -- residue 6: duplicate [ ND1] atoms (total 2)
> > > -- residue 6: duplicate [ NE2] atoms (total 2)
> > > -- residue 6: duplicate [ O] atoms (total 2)
> > > -- residue 7: duplicate [ N] atoms (total 2)
> > > -- residue 23: duplicate [ CD1] atoms (total 2)
> > > -- residue 23: duplicate [ CG1] atoms (total 2)
> > > -- residue 23: duplicate [ CG2] atoms (total 2)
> > > -- residue 47: duplicate [ CG] atoms (total 2)
> > > -- residue 47: duplicate [ OD1] atoms (total 2)
> > > -- residue 47: duplicate [ OD2] atoms (total 2)
> > > -- residue 48: duplicate [ CD] atoms (total 2)
> > > -- residue 48: duplicate [ CG] atoms (total 2)
> > > -- residue 48: duplicate [ OE1] atoms (total 2)
> > > -- residue 48: duplicate [ OE2] atoms (total 2)
> > > -- residue 58: duplicate [ CD1] atoms (total 2)
> > > -- residue 58: duplicate [ CD2] atoms (total 2)
> > > -- residue 80: duplicate [ CD1] atoms (total 2)
> > > -- residue 80: duplicate [ CD2] atoms (total 2)
> > > -- residue 114: duplicate [ C] atoms (total 2)
> > > -- residue 114: duplicate [ CA] atoms (total 2)
> > > -- residue 114: duplicate [ CB] atoms (total 2)
> > > -- residue 114: duplicate [ CD2] atoms (total 2)
> > > -- residue 114: duplicate [ CE1] atoms (total 2)
> > > -- residue 114: duplicate [ CG] atoms (total 2)
> > > -- residue 114: duplicate [ N] atoms (total 2)
> > > -- residue 114: duplicate [ ND1] atoms (total 2)
> > > -- residue 114: duplicate [ NE2] atoms (total 2)
> > > -- residue 114: duplicate [ O] atoms (total 2)
> > > -- residue 155: duplicate [ CG] atoms (total 2)
> > > -- residue 155: duplicate [ OD1] atoms (total 2)
> > > -- residue 155: duplicate [ OD2] atoms (total 2)
> > > -- residue 166: duplicate [ CD1] atoms (total 2)
> > > -- residue 166: duplicate [ CD2] atoms (total 2)
> > > -- residue 188: duplicate [ CD1] atoms (total 2)
> > > -- residue 188: duplicate [ CD2] atoms (total 2)
> > >
> > > Warning: Atom names in each residue should be unique.
> > > (Same-name atoms are handled by using the first
> > > occurrence and by ignoring the rest.
> > > Frequently duplicate atom names stem from alternate
> > > conformations in the PDB file.)
> > >
> > > Unknown residue: CU number: 216 type: Terminal/beginning
> > > ..relaxing end constraints to try for a dbase match
> > > -no luck
> > > Unknown residue: MPD number: 217 type: Nonterminal
> > > Unknown residue: MPD number: 218 type: Nonterminal
> > > Unknown residue: MPD number: 219 type: Nonterminal
> > > Unknown residue: MPD number: 220 type: Terminal/last
> > > ..relaxing end constraints to try for a dbase match
> > > -no luck
> > > Unknown residue: CU number: 221 type: Terminal/beginning
> > > ..relaxing end constraints to try for a dbase match
> > > -no luck
> > > Unknown residue: MPD number: 222 type: Nonterminal
> > > Unknown residue: MPD number: 223 type: Nonterminal
> > > Unknown residue: MPD number: 224 type: Terminal/last
> > > ..relaxing end constraints to try for a dbase match
> > > -no luck
> > > Creating new UNIT for residue: CU sequence: 217
> > > Created a new atom named: CU within residue: .R<CU 217>
> > > Creating new UNIT for residue: MPD sequence: 218
> > > Created a new atom named: C1 within residue: .R<MPD 218>
> > > Created a new atom named: C2 within residue: .R<MPD 218>
> > > Created a new atom named: O2 within residue: .R<MPD 218>
> > > Created a new atom named: CM within residue: .R<MPD 218>
> > > Created a new atom named: C3 within residue: .R<MPD 218>
> > > Created a new atom named: C4 within residue: .R<MPD 218>
> > > Created a new atom named: O4 within residue: .R<MPD 218>
> > > Created a new atom named: C5 within residue: .R<MPD 218>
> > > Creating new UNIT for residue: MPD sequence: 219
> > > Created a new atom named: C1 within residue: .R<MPD 219>
> > > Created a new atom named: C2 within residue: .R<MPD 219>
> > > Created a new atom named: O2 within residue: .R<MPD 219>
> > > Created a new atom named: CM within residue: .R<MPD 219>
> > > Created a new atom named: C3 within residue: .R<MPD 219>
> > > Created a new atom named: C4 within residue: .R<MPD 219>
> > > Created a new atom named: O4 within residue: .R<MPD 219>
> > > Created a new atom named: C5 within residue: .R<MPD 219>
> > > Creating new UNIT for residue: MPD sequence: 220
> > > Created a new atom named: C1 within residue: .R<MPD 220>
> > > Created a new atom named: C2 within residue: .R<MPD 220>
> > > Created a new atom named: O2 within residue: .R<MPD 220>
> > > Created a new atom named: CM within residue: .R<MPD 220>
> > > Created a new atom named: C3 within residue: .R<MPD 220>
> > > Created a new atom named: C4 within residue: .R<MPD 220>
> > > Created a new atom named: O4 within residue: .R<MPD 220>
> > > Created a new atom named: C5 within residue: .R<MPD 220>
> > > Creating new UNIT for residue: MPD sequence: 221
> > > Created a new atom named: C1 within residue: .R<MPD 221>
> > > Created a new atom named: C2 within residue: .R<MPD 221>
> > > Created a new atom named: O2 within residue: .R<MPD 221>
> > > Created a new atom named: CM within residue: .R<MPD 221>
> > > Created a new atom named: C3 within residue: .R<MPD 221>
> > > Created a new atom named: C4 within residue: .R<MPD 221>
> > > Created a new atom named: O4 within residue: .R<MPD 221>
> > > Created a new atom named: C5 within residue: .R<MPD 221>
> > > Creating new UNIT for residue: CU sequence: 222
> > > Created a new atom named: CU within residue: .R<CU 222>
> > > Creating new UNIT for residue: MPD sequence: 223
> > > Created a new atom named: C1 within residue: .R<MPD 223>
> > > Created a new atom named: C2 within residue: .R<MPD 223>
> > > Created a new atom named: O2 within residue: .R<MPD 223>
> > > Created a new atom named: CM within residue: .R<MPD 223>
> > > Created a new atom named: C3 within residue: .R<MPD 223>
> > > Created a new atom named: C4 within residue: .R<MPD 223>
> > > Created a new atom named: O4 within residue: .R<MPD 223>
> > > Created a new atom named: C5 within residue: .R<MPD 223>
> > > Creating new UNIT for residue: MPD sequence: 224
> > > Created a new atom named: C1 within residue: .R<MPD 224>
> > > Created a new atom named: C2 within residue: .R<MPD 224>
> > > Created a new atom named: O2 within residue: .R<MPD 224>
> > > Created a new atom named: CM within residue: .R<MPD 224>
> > > Created a new atom named: C3 within residue: .R<MPD 224>
> > > Created a new atom named: C4 within residue: .R<MPD 224>
> > > Created a new atom named: O4 within residue: .R<MPD 224>
> > > Created a new atom named: C5 within residue: .R<MPD 224>
> > > Creating new UNIT for residue: MPD sequence: 225
> > > Created a new atom named: C1 within residue: .R<MPD 225>
> > > Created a new atom named: C2 within residue: .R<MPD 225>
> > > Created a new atom named: O2 within residue: .R<MPD 225>
> > > Created a new atom named: CM within residue: .R<MPD 225>
> > > Created a new atom named: C3 within residue: .R<MPD 225>
> > > Created a new atom named: C4 within residue: .R<MPD 225>
> > > Created a new atom named: O4 within residue: .R<MPD 225>
> > > Created a new atom named: C5 within residue: .R<MPD 225>
> > > total atoms in file: 1886
> > > Leap added 1946 missing atoms according to residue templates:
> > > 1946 H / lone pairs
> > > The file contained 58 atoms not in residue templates
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------------------------
> Dongshan Wei, Dr.
> Chongqing Institute of Green and Intelligent Technology, CAS
> 85 Jinyu Ave, Yubei Area, Chongqing 401120, China
> Email: dswei.cigit.ac.cn <dswei.cigit.cas.cn>
> Phone: (+86) 23-63063762
> ---------------------------------------------------------
>
>
> ------------------------------
>
> Message: 22
> Date: Thu, 13 Jun 2013 09:17:27 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Step by step tutorial to using Ptraj in
> generating DCCM
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOa3a-E8BnRg2wrzqw=xVjtz=7PUhuyh9aeqEcctBwBi1w.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> I think what you want is the correlation matrix calculation or 'matrix
> correl'. This calculates matrix entries as:
>
> Mij = (<ri * rj> - <ri><rj>) / sqrt( (<ri^2> - <ri>^2) * (<rj^2> - <rj>^2) )
>
> which I believe is the definition commonly defined as a dynamic
> cross-correlation map (DCCM). In order to get meaningful results you
> should probably RMS-fit your structures to an average structure first
> (otherwise translational and rotational motions will dominate). So a
> typical procedure might go (assuming you have a previously calculated
> average reference structure or something similar):
>
> reference average.rst7
> trajin traj.nc
> rms reference .CA
> matrix correl .CA out matrix_correl_CA.dat
>
> If you would like the output by residue specify the 'byres' keyword in
> the 'matrix' command. Hope this helps,
>
> -Dan
>
>
> On Wed, Jun 12, 2013 at 7:22 PM, #YIP YEW MUN# <YIPY0005.e.ntu.edu.sg> wrote:
> > Hi,
> >
> > I wish to ask the steps to using ptraj in generating DCCM for alpha-C in
> > proteins. I tried searching the net for a tutorial or some sort but to no
> > avail. I would appreciate if there is someone to list out the step-by-step
> > way to generating DCCM.
> >
> > Many thanks.
> >
> > --
> > Regards
> > Yip Yew Mun
> > Chemistry and Biological Chemistry
> > School of Physical and Mathematical Sciences
> > Nanyang Technological University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
>
>
> ------------------------------
>
> Message: 23
> Date: Thu, 13 Jun 2013 13:43:07 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] bad atom type: N3 (In MMGBSA decomp calculations)
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3p7J7ahARmpirmme2jizw2-6qGyBGLERovsP9uZnf5eRw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Can you post your MMPBSA.py input file?
>
>
> On Wed, Jun 12, 2013 at 6:38 PM, Jason Slingsby <jason.slingsby.gmail.com>wrote:
>
> > Dear Amber Users,
> >
> > I am trying to run a decomposition analysis on a protein and keep running
> > into the following error:
> >
> > bad atom type: N3
> > CalcError: /amber12/bin/sander failed with prmtop complex.prmtop!
> >
> > I have successfully run a different system through the decomp which also
> > contained N3 atom types. Looking through the .prmtops I see no differences
> > in the way that the amino acids containing type N3 were written between the
> > two different systems.
> >
> > Any ideas as to what could be causing this error? The protein that isn't
> > working is a channel made of 5 subunits. I noticed that all subunits begin
> > with N3 (on SER and THR residues) Could this have something to do with it
> > or is it some other issue?
> >
> > Thanks,
> > Jason
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
>
> ------------------------------
>
> Message: 24
> Date: Thu, 13 Jun 2013 12:59:09 -0500
> From: Manikanthan Bhavaraju <manikanthanbhavaraju.gmail.com>
> Subject: [AMBER] amber2accent perl script
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAL=+FKpQii21p3Fk-C6baZOgUuD3jYNnJTWKqShJwdz0qAMs5Q.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Amber users,
>
> I want to convert Amber's trajectory file into Bond-Angle-Torsion
> coordinates (BAT) using amber2accent perl script. However, I am unable to
> download the script from the respective website. I was wondering if
> anybody has the copy of the script and could be able to provide me.
>
> Thanks in advance,
> mani
> --
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 541, Issue 1
> *************************************
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Received on Fri Jun 14 2013 - 04:00:02 PDT
