[gmx-users] Analaysis

‪Mohammad Roostaie‬ ‪ mohammad.r0325 at yahoo.com
Mon Dec 12 06:58:09 CET 2016

Thank you very much Justin

      From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org 
 Sent: Sunday, 11 December 2016, 18:15:01
 Subject: Re: [gmx-users] Analaysis

On 12/11/16 1:01 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi Gromacs users, I want to obtain the percentage of helicity of a peptide
> with respect to time after the simulation, how can I get it? I used the "gmx
> helix" and "gmx do_dssp" commands, but I could not get it. In addition, I

The last line in scount.xvg from gmx do_dssp gives you this.

> want to get the number of clusters and contact area of two particles with
> respect to time, and I used "gmx clustsize" and "gmx mindist" commands, but I
> still cannot get these factors. can you please help me figure this out? Thank

gmx clustsize has output options for number of clusters, cluster size, 
distribution, etc.

If you want contact area, use gmx sasa with appropriate index groups.



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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