[gmx-users] extending simulation without cpt file

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 4 00:31:37 CET 2010

Yongchul Chung wrote:
> 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?

There is no bug here.  You're using tpbconv wrong.  If you don't provide it the 
.trr and .edr files corresponding to the last time frame, you're going to end up 
with a .tpr file that contains the full run time, instead of picking up from the 
last frame, since tpbconv has no knowledge that it exists.


If you tell tpbconv to extend a simulation by 102000 ps with no other 
information, it assumes you're starting from 0.


> Thanks,
> Greg


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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