[gmx-users] Problem with continuation of simulation

[Florian Haberl]

Hi,

On Tuesday 06 June 2006 11:10, Sridhar Acharya wrote:
> Hello,
>
> I had carried out a 20ns protein simulation on Gromacs v3.2.1. Later I
> continued the simulation on Gromacs v3.3.
> I ran the following command supplying the energy file and trajectory
> file. But the program gave error and stopped (log message is given below).

Is your tpbconv from version 3.2.1 or 3.31?
I would sugguest you take this from version 3.2 and mdrun from 3.3

>
> Since I read that supply of energy file is not absolutely required. I
> again ran tpbconv without -e option for another 10ns. This time the
> program ran with the warning message that the continuation will not be
> exact.
> "WARNING: The simulation uses pressure and/or Nose-Hoover temperature
> coupling,
>          the continuation will only be exact when an energy file is
> supplied".
>
> When I plotted the trajectory of the Potential energy, I found the
> difference, with PE much below than the previous simulation (PE dropped
> from -559000 to -561000). Can I use the data of this additional
> simulation, or is it a drastic variation, that I need to take care of?
>
> Thank you,
> expecting your suggessions.
>
> ###########################################################################
>########### [msridhar at cdfd-grid-node10 TRAJEC_WT]$  tpbconv  -s
> ../OTHERS_WT/b4md_1cyp_WT.tpr -f rerereafter15_WT.trr  -e
> ../OTHERS_WT/rerereafter15_WT.edr -o new.tpr -until 30000
>
>                        :-)  G  R  O  M  A  C  S  (-:
>
>                   Gromacs Runs On Most of All Computer Systems
>
>                              :-)  VERSION 3.3  (-:
>
>       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 ../OTHERS_WT/b4md_1cyp_WT.tpr  Input        Generic run input: tpr tpb
>                                    tpa xml
>   -f rerereafter15_WT.trr  Input, Opt!  Full precision trajectory: trr trj
>   -e ../OTHERS_WT/rerereafter15_WT.edr  Input, Opt!  Generic energy: edr
> ene -n      index.ndx  Input, Opt.  Index file
>   -o        new.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  30000  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 ../OTHERS_WT/b4md_1cyp_WT.tpr
> Reading file ../OTHERS_WT/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single
> precision) Note: tpx file_version 24, software version 40
> Note: nLincsIter not in run input file, setting it to 1
> Modifying ir->bUncStart to TRUE
>
> READING COORDS, VELS AND BOX FROM TRAJECTORY rerereafter15_WT.trr...
>
> trn version: GMX_trn_file (single precision)
> Read frame    684: step 341344 time 20000.000
>
> Using frame of step 341344 time 20000
> Opened ../OTHERS_WT/rerereafter15_WT.edr as single precision energy file
> Reading frame     60 time 19917.312
> -------------------------------------------------------
> Program tpbconv, VERSION 3.3
> Source code file: enxio.c, line: 358
>
> Fatal error:
> Could not find energy term named 'Pcoupl-Mu-XX'
> -------------------------------------------------------
>
> "Stop Drinking My Beer !" (The Amps)
> ###########################################################################
>##############

Greetings,

Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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