I don't see any error message in your email, so it's impossible to diagnose
remotely. Can you find any error message from the standard output/standard
error streams? A cluster should save those to separate files if that's
where you're running.
Another common suggestion is to run with ntpr=1 and take a look at what
happens at each step to narrow in on what's happening.
Good luck,
Jason
On Thu, Mar 24, 2011 at 10:47 AM, vani panguluri <vanipanguluri.gmail.com>wrote:
> 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' /
> BlAH
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 24 2011 - 11:00:05 PDT
