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. > > ########################################################################### >########### [EMAIL PROTECTED] 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 ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
