[gmx-users] Extending simulation problem.

Justin Lemkul jalemkul at vt.edu
Wed Aug 20 19:18:24 CEST 2014

On 8/20/14, 6:33 AM, Dawid das wrote:
> Dear Gromacs experts,
> I googled for answer and I found these:
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
> http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_10000_ps
> but still I am confused about what happens in my simulation. I did 5 ns
> simulation and I would like to add extra 5 ns on top of that so that new
> results (energies, temperature, trajectory, etc.) will be appended to
> already existing files after first 5 ns simulation. Now I used this command
> to run MD simulation for the first time:
> \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e
> mCherry7-npt-md.edr > $CURDIR/mCherry7-npt-md.log 2>&1
> After this in the same directory I run:
> tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr
> \$MDRUN -s npt-md-ext.tpr -cpi state.cpt
> I tried both state.cpt and prev_state.cpt and the beginning of new
> simulation looks exactly the same
> that means temperature, energies, etc. are the same as if I started
> from 0ns step, not from 5ns step of
> previous simulation. What can cause that? Is it because of used files
> names or I did something else wrong?

What does the .log file say?  It should clearly indicate if the restart was done 
by reading in the checkpoint file.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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