[gmx-users] gmx convert-tpr, gmx check Q ?
jalemkul at vt.edu
Tue Apr 12 20:43:44 CEST 2016
On 4/12/16 9:24 AM, badamkhatan togoldor wrote:
> Thank you for reply of Justin. So as I understood from there no need to convert-tpr and just do it like,
> gmx mdrun -deffnm pro$ -cpi pro1.cpt -append
> That's it ?
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Sent: Tuesday, 12 April 2016, 15:23
> Subject: Re: [gmx-users] gmx convert-tpr, gmx check Q ?
> 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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