[gmx-users] Restarting crashed simmulation.

Justin Lemkul jalemkul at vt.edu
Thu May 10 14:08:15 CEST 2018

On 5/10/18 7:08 AM, neelam wafa wrote:
> Hi gmx users!
> I am running a 5ns md simmulation of a protein with 2500000 steps. It
> crashed at  1360000 steps due to some power problem. Now I want to continue
> this simmulation. In the manual following command is given:
> mdrun -s topol.tpr -cpi state.cpt
> but I am confused which file is state.cpt. I have got two cpt files
> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

Look at the time stamps of the files and inspect their contents with gmx 
check. You will see an obvious difference in what they contain. Also 
consult the mdrun help info, which specifically addresses your question.

> Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?

Yes, because that file is only produced from the last step.

> Also do I need to specify  -append flag or not? I am using version 5.1.5

-append has been the default option for many years. Again, see the mdrun 
help description.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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