[gmx-users] Extending simulation, quick question

Justin Lemkul jalemkul at vt.edu
Mon Dec 19 02:32:59 CET 2016

On 12/18/16 9:53 AM, Dario Akaberi wrote:
> Hello,
> I have a quick question.
> I've extended a simulation using the commnds:
> convert-tpr -s md_3.tpr -extend 10000 -o md_3_next.tpr
> followed by
> mdrun -s md_3_next.tpr  -cpi md_3_prev.cpt
> My questions are:
> 1) should I use the md_3_prev.cpt file or the md_3.cpt file? are these two
> file the same if the simulation ended without problems?

Use gmx check to see what the differences are, and read the relevant mdrun help 
text, which describes what these files are and why there are two of them.

> 2) Now for the following analysis I have to use the new .tpr file that i
> generated with convert-tpr right? (in this case md_3_next.tpr)

They differ only in the number of steps, so for the purposes of analysis there 
is no difference.  You can again use gmx check -s1 -s2 to compare them.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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