[gmx-users] Calculating Distance

Christopher Neale chris.neale at alum.utoronto.ca
Tue May 17 21:35:48 CEST 2016

In case anybody else finds the gmx distance input as confusing as I did... if you want to get the distance between the center of mass of the peptide and the center of mass of the SDS, you would first create Protein and SDS groups in an index file (say they are groups 1 and 2), then send that to "gmx distance" and you would type "com of group 1 plus com of group 2" interactively or script the piping of this text into "gmx distance"

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: 16 May 2016 07:51:51
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Calculating Distance

On 5/16/16 3:20 AM, Sanket Ghawali wrote:
> Dear, gmx-users,
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The simulation was
> performed for 100ns
> When I visualize the trajectory in VMD, the peptide moves to the SDS
> interface where initially it was placed in the center,  the results
> are as expected. I would like to calculate the distance the peptide
> has traveled or moved from the center to the interface
> Any suggestions on how to go about doing this?

Calculating distances is what the gmx distance program is for.  Simply obtain
the COM distance between the micelle and peptide (or any subset of atoms that
makes sense).



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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