[gmx-users] countinuation run problem

[David van der Spoel]

Anthony Cruz wrote:
> HI:
> Yesterday one of my simulation crash. I check the log file. This are the last 
> lines of the file:
> 
> Step           Time         Lambda
>         6109000    12218.00098        0.00000
> 
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.058792   1139   1140   0.007195
>         After LINCS         0.000126     75     77   0.000021
> 
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     3.95784e+03    1.69609e+03    1.21916e+03    7.85820e+02    3.20988e+04
>         LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)      Potential
>     2.49591e+05   -7.40570e+03   -1.58839e+06   -2.16905e+05   -1.52336e+06
>     Kinetic En.   Total Energy    Temperature Pressure (bar)
>     2.74080e+05   -1.24927e+06    2.97765e+02   -8.69934e+00
> 
> Then I try to use tpbconvert to continue the simulation by the following 
> command:
> 
> -bash-2.05b$ tpbconv -f 1scnMD_MV.trr -e 1scn_MD_ENER.edr -s 1scn_MD_TPR.tpr 
> -o 1scn_MD_TPR_CONT.tpr
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>                                Grunge ROck MAChoS
> 
>                             :-)  VERSION 3.2.1  (-:
> 
> 
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2004, The GROMACS development team,
>             check out http://www.gromacs.org for more information.
> 
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
> 
>                                :-)  tpbconv  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -s 1scn_MD_TPR.tpr  Input        Generic run input: tpr tpb tpa xml
>   -f  1scnMD_MV.trr  Input, Opt!  Full precision trajectory: trr trj
>   -e 1scn_MD_ENER.edr  Input, Opt!  Generic energy: edr ene
>   -n      index.ndx  Input, Opt.  Index file
>   -o 1scn_MD_TPR_CONT.tpr  Output       Generic run input: tpr tpb tpa xml
> 
>       Option   Type  Value  Description
> ------------------------------------------------------
>       -[no]h   bool     no  Print help info and quit
>       -[no]X   bool     no  Use dialog box GUI to edit command line options
>        -nice    int      0  Set the nicelevel
>        -time   real     -1  Continue from frame at this time (ps) instead of
>                             the last frame
>      -extend   real      0  Extend runtime by this amount (ps)
>       -until   real      0  Extend runtime until this ending time (ps)
>   -[no]zeroq   bool     no  Set the charges of a group (from the index) to
>                             zero
> -[no]unconstrained
>                bool    yes  For a continuous trajectory, the constraints
>                             should not be solved before the first step
>                             (default)
> 
> Reading toplogy and shit from 1scn_MD_TPR.tpr
> Reading file 1scn_MD_TPR.tpr, VERSION 3.2.1 (single precision)
> Modifying ir->bUncStart to TRUE
> 
> READING COORDS, VELS AND BOX FROM TRAJECTORY 1scnMD_MV.trr...
> 
> trn version: GMX_trn_file (single precision)
> Read frame   2334: step 1166500 time 2333.000
> 
> Using frame of step 1166500 time 2333
> Opened 1scn_MD_ENER.edr as single precision energy file
> Reading frame   2330 time 2330.000
> 
> READ 3 PRESSURE COUPLING MU'S FROM 1scn_MD_ENER.edr
> 
> 
> READ 4 TEMPERATURE COUPLING LAMBDAS FROM 1scn_MD_ENER.edr
> 
> 10083500 steps (20167 ps) remaining from first run.
> Writing statusfile with starting step    1166500 and length   10083500 
> steps...
>                                  time   2333.000 and length  20167.000 ps
> 
> Back Off! I just backed up 1scn_MD_TPR_CONT.tpr to ./#1scn_MD_TPR_CONT.tpr.1#
> 
> gcq#162: "Rub It Right Accross Your Eyes" (F. Zappa)
> 
> 
> The total time of my simulation is 22ns and as the log file said it runs for 
> Step           Time         Lambda
>         6109000    12218.00098        0.00000
> but  tpbconv use time   2333.000 and length  20167.000 ps for the continue 
> file. The output control in my mdp file are the fallowing:
>   
>   ; Output Control
> nstxout             =  500
> nstvout             =  500
> nstfout             =  0
> nstlog              =  500
> nstenergy           =  500
> 
> 
> What is wrong?  Why do not continue at the last frame described in the log 
> file?? 
> 
> Best regards 
> Anthony
>   
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run gmxcheck on your edr and trr files. Sometimes the OS buffers these 
files.

maybe you have a full disk.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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