[gmx-users] Umbrella Samling Alteration

Alexander Law alexander.law at pg.canterbury.ac.nz
Thu Feb 5 04:39:48 CET 2015

Hi Justin

The runs have started but they are not currently running, as in they were cancelled and I can start them up again using the .cpt file. Is it still possible to alter add the -nsteps in this case?

Many Thanks,
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Tuesday, February 03, 2015 1:51 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Umbrella Samling Alteration

On 2/1/15 11:22 PM, Alexander Law wrote:
> Dear Gromacs Users
> I am currently running the series of simulations using the following command:
> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
> I wish to lessen the amount of time for each of these simulations from 10 ns to 6 ns. These simulations are already up to around 5 ns, is it possible to change the time to 6 ns without altering the md_umbrella.mdp file and starting agin? Also, will this reduction have any major impacts on the quality/efficacy of the data?

Use mdrun command-line option -nsteps to override the number of steps specified
in the .tpr file, but you can't do this if the runs are in progress.



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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