[gmx-users] interrupt simulation

Justin Lemkul jalemkul at vt.edu
Wed Aug 27 13:49:05 CEST 2014

On 8/27/14, 6:24 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)

Either the simulation crashed, the filesystem caused a problem, or queue limits 
caused termination of the job.

> ** 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.

If the original .tpr file was set up for 10 ns, you don't need to do this.  Just 
issue the same mdrun command as before, but add -cpi (whatever the checkpoint 
filename is) and -append.

> 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.

mdrun will not overwrite anything, ever.  All Gromacs programs back up existing 
files with the same name, but the use of -append will cause mdrun to append to 
existing output if it can.



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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