[gmx-users] gmx convert-tpr, gmx check Q ?

Justin Lemkul jalemkul at vt.edu
Tue Apr 12 14:23:28 CEST 2016

On 4/12/16 8:16 AM, badamkhatan togoldor wrote:
> Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr
> and gmx check.  I have a little bit doubt in that.  Simulation was
> calculating 5.000.000 steps, 10ns and it has stopped due to the some cluster
> time limit. So I want to continue it from that stopped step. So, gmx
> convert-tpr -s pro.tpr -f pro.trr -e pro.edr -o pro1.tpr -until 10000 ( it

There is no need to invoke convert-tpr for a run that stopped prematurely.

> means that when checked the gmx check the .tpr file it says 4688 step and 1
> ps. From this step until finish to 10 ps?)     And also 10,000 ps  is 10 ns
> right? then why gmx check gave me the 1 ps ? or is it 1 ns ?

The timestep here (in ps, as noted) is the interval between frames.

> Item        #frames Timestep (ps)
 > Step          4688    1
 > Time          4688    1
 > Lambda        4688    1
> Coords        4688    1
> gmx mdrun -deffnm $pro -append -cpi which check point file I should apply
> pro.cpt  OR pro_prev.cpt ? I would highly appreciate for any answers! Thanks

What does gmx check tell you about the contents of each of these?  The help info 
for mdrun also explains the checkpointing mechanism and the difference in these 
files, so start by reading that.



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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