I am asking that after termination of MD run did you try to run it again or
if you have another computing system then run your MD simulation in that system.
your output file not showing error so may be it is your error.
you can do one more thing if you have earlier successfully completed MD run then
run this to same cluster and check whether its runing or not.
> Hi sangita,
>
> Did you heard about the loni Clusters in that i am using QueenBee it runs on
> 8 processors , but it was stopping in the middle.....
> I had mentioned that one too run 25000 steps but it was terminating in the
> middle i.e; after completing the 15000 steps......
> why it was terminating like that and also one thing i forgot to mention that
> i am using secure shell to connect remotely and work on that system.......
> Have you rerun MD simulation? (i Can't understand what you are asking)
>
> Regards,
> Vani
>
>
>
>
>
>
> On Thu, Mar 24, 2011 at 1:28 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>> Hello Vani
>>
>> Have you rerun MD simulation? May be it is your cluster,s or the system
>> where
>> you are running error.
>>
>>
>> > hello amber users,
>> >
>> > I am using the sander for md simulation during the process it was
>> > terminating in the middle and the out in the heat.out file was like this
>> > *sander -O -i heat.in -o heat.out -p pdb1k4u_apo2_sol.prmtop -c min.rst
>> -r
>> > heat.rst -x heat.mdcrd -ref min.rst*
>> >
>> > *Output:-*
>> > -------------------------------------------------------
>> > Amber 11 SANDER 2010
>> > -------------------------------------------------------
>> >
>> > | Run on 03/24/2011 at 10:21:13
>> > [-O]verwriting output
>> >
>> > File Assignments:
>> > | MDIN: heat.in
>> > | MDOUT: heat.out
>> > |INPCRD: min.rst
>> > | PARM: pdb1k4u_apo2_sol.prmtop
>> > |RESTRT: heat.rst
>> > | REFC: min.rst
>> > | MDVEL: mdvel
>> > | MDEN: mden
>> > | MDCRD: heat.mdcrd
>> > |MDINFO: mdinfo
>> > | MTMD: mtmd
>> > |INPDIP: inpdip
>> > |RSTDIP: rstdip
>> >
>> > |INPTRA: inptraj
>> > |
>> >
>> > Here is the input file:
>> >
>> > heat pdb1k4u_apo2
>> > &cntrl
>> > imin=0,irest=0,ntx=1,
>> > nstlim=25000,dt=0.002,
>> > ntc=2,ntf=2,
>> > cut=8.0, ntb=1,
>> > ntpr=500, ntwx=500,
>> > ntt=3, gamma_ln=2.0,
>> > tempi=0.0, temp0=300.0,
>> > ntr=1,
>> > nmropt=1
>> > /
>> > &wt TYPE='TEMP0', istep1=0, istep2=25000,
>> > value1=0.1, value2=300.0, /
>> > &wt TYPE='END' /
>>
>>
>> what is ...BlAH.... in your input file?
>>
>> > 2.0
>> > RES 1 242
>> > END
>> > END
>> >
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 1. RESOURCE USE:
>> >
>> --------------------------------------------------------------------------------
>> >
>> > | Flags:
>> > getting new box info from bottom of inpcrd
>> > | INFO: Old style inpcrd file read
>> >
>> > | peek_ewald_inpcrd: Box info found
>> > |Largest sphere to fit in unit cell has radius = 32.368
>> > | New format PARM file being parsed.
>> > | Version = 1.000 Date = 03/23/11 Time = 00:31:52
>> > NATOM = 24182 NTYPES = 16 NBONH = 23441 MBONA = 753
>> > NTHETH = 1721 MTHETA = 1017 NPHIH = 3206 MPHIA = 2555
>> > NHPARM = 0 NPARM = 0 NNB = 38524 NRES = 7659
>> > NBONA = 753 NTHETA = 1017 NPHIA = 2555 NUMBND = 47
>> > NUMANG = 87 NPTRA = 41 NATYP = 35 NPHB = 1
>> > IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
>> > NCOPY = 0
>> >
>> >
>> > | Memory Use Allocated
>> > | Real 1342688
>> > | Hollerith 80207
>> > | Integer 828340
>> > | Max Pairs 8060666
>> > | nblistReal 290184
>> > | nblist Int 1300633
>> > | Total 52873 kbytes
>> >
>> > | Note: 1-4 EEL scale factors were NOT found in the topology file.
>> > | Using default value of 1.2.
>> >
>> > | Note: 1-4 VDW scale factors were NOT found in the topology file.
>> > | Using default value of 2.0.
>> > | Duplicated 0 dihedrals
>> > | Duplicated 0 dihedrals
>> >
>> > BOX TYPE: RECTILINEAR
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 2. CONTROL DATA FOR THE RUN
>> >
>> --------------------------------------------------------------------------------
>> >
>> >
>> >
>> > General flags:
>> > imin = 0, nmropt = 1
>> >
>> > Nature and format of input:
>> > ntx = 1, irest = 0, ntrx = 1
>> >
>> > Nature and format of output:
>> > ntxo = 1, ntpr = 500, ntrx = 1, ntwr =
>> > 500
>> > iwrap = 0, ntwx = 500, ntwv = 0, ntwe =
>> > 0
>> > ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
>> > 0
>> >
>> > Potential function:
>> > ntf = 2, ntb = 1, 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 = 1
>> >
>> > Molecular dynamics:
>> > nstlim = 25000, nscm = 0, nrespa = 1
>> > t = 0.00000, dt = 0.00200, vlimit = 20.00000
>> >
>> > Langevin dynamics temperature regulation:
>> > ig = 71277
>> > temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
>> >
>> > SHAKE:
>> > ntc = 2, jfastw = 0
>> > tol = 0.00001
>> >
>> > NMR refinement options:
>> > iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
>> > 1
>> > scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
>> >
>> > Ewald parameters:
>> > verbose = 0, ew_type = 0, nbflag = 1, use_pme =
>> > 1
>> > vdwmeth = 1, eedmeth = 1, netfrc = 1
>> > Box X = 64.737 Box Y = 70.948 Box Z = 67.136
>> > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
>> > NFFT1 = 64 NFFT2 = 72 NFFT3 = 72
>> > Cutoff= 8.000 Tol =0.100E-04
>> > Ewald Coefficient = 0.34864
>> > Interpolation order = 4
>> >
>> > LOADING THE CONSTRAINED ATOMS AS GROUPS
>> >
>> >
>> > 5. REFERENCE ATOM COORDINATES
>> >
>> >
>> > ----- READING GROUP 1; TITLE:
>> > BlAH
>> >
>> > GROUP 1 HAS HARMONIC CONSTRAINTS 2.00000
>> > GRP 1 RES 1 TO 242
>> > Number of atoms in this group = 1931
>> > ----- END OF GROUP READ -----
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 3. ATOMIC COORDINATES AND VELOCITIES
>> >
>> --------------------------------------------------------------------------------
>> >
>> >
>> > begin time read from input coords = 0.000 ps
>> >
>> >
>> >
>> > Begin reading energy term weight changes/NMR restraints
>> > WEIGHT CHANGES:
>> > TEMP0 0 25000 0.100000 300.000000 0 0
>> >
>> > RESTRAINTS:
>> > No valid redirection requests found
>> > ** No restraint defined **
>> >
>> > Done reading weight changes/NMR restraints
>> >
>> >
>> > Number of triangulated 3-point waters found: 7564
>> >
>> > Sum of charges from parm topology file = -3.00000003
>> > Assuming uniform neutralizing plasma
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 4. RESULTS
>> >
>> --------------------------------------------------------------------------------
>> >
>> > | # of SOLUTE degrees of freedom (RNDFP): 49105.
>> > | # of SOLVENT degrees of freedom (RNDFS): 0.
>> > | NDFMIN = 49105. NUM_NOSHAKE = 0 CORRECTED RNDFP =
>> 49105.
>> > | TOTAL # of degrees of freedom (RNDF) = 49105.
>> > ---------------------------------------------------
>> > 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 = 0.8314E-11 at 2.736960
>> > ---------------------------------------------------
>> > | Local SIZE OF NONBOND LIST = 4134189
>> > | TOTAL SIZE OF NONBOND LIST = 4134189
>> >
>> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
>> > 0.0
>> > Etot = -67866.2635 EKtot = 0.0000 EPtot =
>> > -67866.2635
>> > BOND = 31.0171 ANGLE = 169.8340 DIHED =
>> > 1090.8243
>> > 1-4 NB = 424.8482 1-4 EEL = 4660.1412 VDWAALS =
>> > 4589.3108
>> > EELEC = -78832.2390 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> > Ewald error estimate: 0.7614E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 47.66 PRESS =
>> > 0.0
>> > Etot = -85453.1115 EKtot = 2325.4435 EPtot =
>> > -87778.5550
>> > BOND = 43.4984 ANGLE = 206.9241 DIHED =
>> > 1002.0524
>> > 1-4 NB = 342.7681 1-4 EEL = 4572.8643 VDWAALS =
>> > 15581.9365
>> > EELEC = -109890.0083 EHBOND = 0.0000 RESTRAINT =
>> > 361.4094
>> > EAMBER (non-restraint) = -88139.9645
>> > Ewald error estimate: 0.2329E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 18.63 PRESS =
>> > 0.0
>> > Etot = -89269.2449 EKtot = 908.9589 EPtot =
>> > -90178.2037
>> > BOND = 41.6598 ANGLE = 205.1703 DIHED =
>> > 1003.6214
>> > 1-4 NB = 345.2256 1-4 EEL = 4582.3395 VDWAALS =
>> > 17090.0126
>> > EELEC = -113778.0157 EHBOND = 0.0000 RESTRAINT =
>> > 331.7828
>> > EAMBER (non-restraint) = -90509.9866
>> > Ewald error estimate: 0.3114E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 1500 TIME(PS) = 3.000 TEMP(K) = 17.59 PRESS =
>> > 0.0
>> > Etot = -89721.9185 EKtot = 858.2083 EPtot =
>> > -90580.1268
>> > BOND = 48.4207 ANGLE = 210.8804 DIHED =
>> > 1001.3563
>> > 1-4 NB = 347.9077 1-4 EEL = 4577.7689 VDWAALS =
>> > 17267.1602
>> > EELEC = -114356.4861 EHBOND = 0.0000 RESTRAINT =
>> > 322.8651
>> > EAMBER (non-restraint) = -90902.9919
>> > Ewald error estimate: 0.1980E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 22.00 PRESS =
>> > 0.0
>> > Etot = -89430.1844 EKtot = 1073.3741 EPtot =
>> > -90503.5585
>> > BOND = 49.6331 ANGLE = 219.5662 DIHED =
>> > 1006.0362
>> > 1-4 NB = 347.5233 1-4 EEL = 4572.7148 VDWAALS =
>> > 17255.5088
>> > EELEC = -114278.2281 EHBOND = 0.0000 RESTRAINT =
>> > 323.6872
>> > EAMBER (non-restraint) = -90827.2457
>> > Ewald error estimate: 0.2090E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 2500 TIME(PS) = 5.000 TEMP(K) = 27.74 PRESS =
>> > 0.0
>> > Etot = -89008.9434 EKtot = 1353.4825 EPtot =
>> > -90362.4259
>> > BOND = 58.4709 ANGLE = 236.9170 DIHED =
>> > 1008.8628
>> > 1-4 NB = 348.7314 1-4 EEL = 4569.0384 VDWAALS =
>> > 17189.9260
>> > EELEC = -114103.0239 EHBOND = 0.0000 RESTRAINT =
>> > 328.6515
>> > EAMBER (non-restraint) = -90691.0774
>> > Ewald error estimate: 0.2593E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 33.60 PRESS =
>> > 0.0
>> > Etot = -88503.6628 EKtot = 1639.3219 EPtot =
>> > -90142.9847
>> > BOND = 65.6348 ANGLE = 245.9596 DIHED =
>> > 1007.8235
>> > 1-4 NB = 349.7460 1-4 EEL = 4572.6333 VDWAALS =
>> > 17019.4238
>> > EELEC = -113744.3925 EHBOND = 0.0000 RESTRAINT =
>> > 340.1869
>> > EAMBER (non-restraint) = -90483.1716
>> > Ewald error estimate: 0.2305E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 3500 TIME(PS) = 7.000 TEMP(K) = 39.08 PRESS =
>> > 0.0
>> > Etot = -88019.0265 EKtot = 1906.5905 EPtot =
>> > -89925.6170
>> > BOND = 63.2188 ANGLE = 256.4110 DIHED =
>> > 1013.9218
>> > 1-4 NB = 348.6459 1-4 EEL = 4587.8149 VDWAALS =
>> > 16991.6064
>> > EELEC = -113525.9987 EHBOND = 0.0000 RESTRAINT =
>> > 338.7630
>> > EAMBER (non-restraint) = -90264.3800
>> > Ewald error estimate: 0.2235E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 44.89 PRESS =
>> > 0.0
>> > Etot = -87487.5513 EKtot = 2190.4102 EPtot =
>> > -89677.9615
>> > BOND = 70.5605 ANGLE = 267.6956 DIHED =
>> > 1013.6091
>> > 1-4 NB = 352.1245 1-4 EEL = 4581.7202 VDWAALS =
>> > 16856.0294
>> > EELEC = -113149.4318 EHBOND = 0.0000 RESTRAINT =
>> > 329.7311
>> > EAMBER (non-restraint) = -90007.6926
>> > Ewald error estimate: 0.2511E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 4500 TIME(PS) = 9.000 TEMP(K) = 51.23 PRESS =
>> > 0.0
>> > Etot = -86949.7560 EKtot = 2499.7782 EPtot =
>> > -89449.5342
>> > BOND = 74.2649 ANGLE = 274.6854 DIHED =
>> > 1010.1647
>> > 1-4 NB = 348.0945 1-4 EEL = 4577.9661 VDWAALS =
>> > 16890.9233
>> > EELEC = -112959.6407 EHBOND = 0.0000 RESTRAINT =
>> > 334.0074
>> > EAMBER (non-restraint) = -89783.5417
>> > Ewald error estimate: 0.2989E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 57.09 PRESS =
>> > 0.0
>> > Etot = -86383.6060 EKtot = 2785.6540 EPtot =
>> > -89169.2600
>> > BOND = 80.1776 ANGLE = 291.2072 DIHED =
>> > 1015.6714
>> > 1-4 NB = 353.7537 1-4 EEL = 4582.2307 VDWAALS =
>> > 16656.8709
>> > EELEC = -112502.2074 EHBOND = 0.0000 RESTRAINT =
>> > 353.0360
>> > EAMBER (non-restraint) = -89522.2960
>> > Ewald error estimate: 0.2921E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 5500 TIME(PS) = 11.000 TEMP(K) = 63.42 PRESS =
>> > 0.0
>> > Etot = -85829.5087 EKtot = 3094.1893 EPtot =
>> > -88923.6981
>> > BOND = 77.0232 ANGLE = 309.7384 DIHED =
>> > 1012.8366
>> > 1-4 NB = 355.3480 1-4 EEL = 4593.4603 VDWAALS =
>> > 16624.8220
>> > EELEC = -112237.7220 EHBOND = 0.0000 RESTRAINT =
>> > 340.7954
>> > EAMBER (non-restraint) = -89264.4935
>> > Ewald error estimate: 0.3281E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 6000 TIME(PS) = 12.000 TEMP(K) = 68.70 PRESS =
>> > 0.0
>> > Etot = -85352.8414 EKtot = 3351.7417 EPtot =
>> > -88704.5830
>> > BOND = 85.4318 ANGLE = 318.3891 DIHED =
>> > 1020.2065
>> > 1-4 NB = 353.6599 1-4 EEL = 4583.8022 VDWAALS =
>> > 16618.2103
>> > EELEC = -112037.8932 EHBOND = 0.0000 RESTRAINT =
>> > 353.6104
>> > EAMBER (non-restraint) = -89058.1934
>> > Ewald error estimate: 0.3406E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 6500 TIME(PS) = 13.000 TEMP(K) = 75.35 PRESS =
>> > 0.0
>> > Etot = -84795.5885 EKtot = 3676.5201 EPtot =
>> > -88472.1086
>> > BOND = 93.3939 ANGLE = 331.9302 DIHED =
>> > 1019.2704
>> > 1-4 NB = 354.4867 1-4 EEL = 4586.6428 VDWAALS =
>> > 16343.5169
>> > EELEC = -111568.0050 EHBOND = 0.0000 RESTRAINT =
>> > 366.6556
>> > EAMBER (non-restraint) = -88838.7642
>> > Ewald error estimate: 0.2858E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 7000 TIME(PS) = 14.000 TEMP(K) = 81.70 PRESS =
>> > 0.0
>> > Etot = -84231.4324 EKtot = 3986.2318 EPtot =
>> > -88217.6642
>> > BOND = 91.0481 ANGLE = 331.4721 DIHED =
>> > 1022.4532
>> > 1-4 NB = 357.9641 1-4 EEL = 4573.0827 VDWAALS =
>> > 16436.7602
>> > EELEC = -111396.0460 EHBOND = 0.0000 RESTRAINT =
>> > 365.6016
>> > EAMBER (non-restraint) = -88583.2658
>> > Ewald error estimate: 0.3731E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 7500 TIME(PS) = 15.000 TEMP(K) = 88.20 PRESS =
>> > 0.0
>> > Etot = -83664.6370 EKtot = 4303.5114 EPtot =
>> > -87968.1484
>> > BOND = 105.3223 ANGLE = 342.3931 DIHED =
>> > 1014.6877
>> > 1-4 NB = 354.3987 1-4 EEL = 4585.1425 VDWAALS =
>> > 16297.6518
>> > EELEC = -111042.1434 EHBOND = 0.0000 RESTRAINT =
>> > 374.3989
>> > EAMBER (non-restraint) = -88342.5473
>> > Ewald error estimate: 0.3299E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 8000 TIME(PS) = 16.000 TEMP(K) = 93.03 PRESS =
>> > 0.0
>> > Etot = -83169.4618 EKtot = 4538.9027 EPtot =
>> > -87708.3646
>> > BOND = 103.9290 ANGLE = 352.7595 DIHED =
>> > 1032.9506
>> > 1-4 NB = 361.4146 1-4 EEL = 4582.1795 VDWAALS =
>> > 16100.3950
>> > EELEC = -110608.5699 EHBOND = 0.0000 RESTRAINT =
>> > 366.5770
>> > EAMBER (non-restraint) = -88074.9416
>> > Ewald error estimate: 0.3722E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 8500 TIME(PS) = 17.000 TEMP(K) = 99.27 PRESS =
>> > 0.0
>> > Etot = -82627.3099 EKtot = 4843.2214 EPtot =
>> > -87470.5313
>> > BOND = 113.5459 ANGLE = 362.8084 DIHED =
>> > 1027.5293
>> > 1-4 NB = 356.3530 1-4 EEL = 4589.4224 VDWAALS =
>> > 16074.2522
>> > EELEC = -110361.3148 EHBOND = 0.0000 RESTRAINT =
>> > 366.8723
>> > EAMBER (non-restraint) = -87837.4036
>> > Ewald error estimate: 0.3323E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> >
>> > NSTEP = 9000 TIME(PS) = 18.000 TEMP(K) = 105.37 PRESS =
>> > 0.0
>> > Etot = -82115.5757 EKtot = 5141.0624 EPtot =
>> > -87256.6381
>> > BOND = 119.1134 ANGLE = 374.1381 DIHED =
>> > 1036.3070
>> > 1-4 NB = 357.5211 1-4 EEL = 4560.3641 VDWAALS =
>> > 16001.5727
>> > EELEC = -110093.3922 EHBOND = 0.0000 RESTRAINT =
>> > 387.7377
>> > EAMBER (non-restraint) = -87644.3759
>> > Ewald error estimate: 0.3482E-03
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>> 0.000
>> >
>> ===============================================================================
>> > "heat.out" 424L, 22218C written
>> >
>> >
>> >
>> > Can any check this and tell me where the problem occurs.
>> >
>> >
>> > Regards,
>> > Vani
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> 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
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 25 2011 - 07:30:02 PDT
