[gmx-users] Interuption Simulation

Justin Lemkul jalemkul at vt.edu
Sun Aug 31 15:00:31 CEST 2014

On 8/30/14, 7:17 AM, Negar Parvizi wrote:
> Dear Gromacs users
> I have submitted a simulation for 10 ns. Now when I started to plot the graphs such as RMSD, I saw that it has stopped at 8 ns. The point is that although the run has stopped before specified time, I see in md.log file the time report for the simulation, the same as report that I get for completed runs. I wanted to know the reason for that? (I should also mention that when I check the upper part of the md.log file, I see that the run has stopped at about 8 ns)
> ** The other thing is about continuing the simulation. For example I want to continue that run for the more 2 ns. I am using gromacs 4.5.4
> I followed the instruction in gromacs website about extending simulations and used these two commands
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt
> **
> now my question is that when I choose timetoextendedby equal to 2000 ps and the simulation finishes,  where will be written the information of that 2 ns, I mean the .gro, .edr and other informations. Should I specify the deffname similar to that I used before for that 8 ns.
> I am not sure whether the gromacs will overwrite the previous files or will edit them and add the information of that 2 ns at the end of previous .gro and .edr and . trj files.

See my previous reply to this question:




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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