[gmx-users] extending simulation without cpt file

Mark Abraham mark.abraham at anu.edu.au
Thu Nov 4 00:36:37 CET 2010

----- Original Message -----
From: Yongchul Chung <yxc169 at case.edu>
Date: Thursday, November 4, 2010 10:28
Subject: [gmx-users] extending simulation without cpt file
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hello gmxers,
> I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands.
> tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr
> mdrun -s topolnew.tpr
> When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem?

You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint.

Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr.


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