[gmx-users] How to get a compressed pull force output from SMD simulation ?

[Justin Lemkul]

On 1/8/16 12:00 AM, Agnivo Gosai wrote:
> Dear Users,
>
> I use GROMACS to do SMD simulation. I have the pullf.xvg file , but it is
> very large. I also have the smd.xtc file. I have used it to calculate the
> COM separation distance between the two pulled groups.
>
> I want to plot force vs COM separation.
>
> Can I calculate the pull force from the .xtc file so that the pull force
> and the COM separation are of same vector lengths? or do I need to add
> something to my .mdp file to be able to do  it ? Like , nstfout ??
>
> I did not download the trr file from the cluster as it is very huge !
>
> Kindly help please.
>

Pulling forces are printed to pullf.xvg at an interval of pull-nstfout in the 
.mdp file.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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