Fw: [gmx-users] make an index file of COM of lipid bilayer

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Jul 16 13:41:27 CEST 2013

Thanks for your reply.
But would you please tell me what is known for the pull_group line? I mean are the atom names or resid-s or residue names or .... know for it?


----- Forwarded Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, July 16, 2013 3:39 PM
Subject: Re: [gmx-users] make an index file of COM of lipid bilayer

On 7/16/13 5:30 AM, Shima Arasteh wrote:
> Hi,
> Would you please let me know how can I make an index file of COM of lipid membrane?
> I guess the position of the COM of the bilayer, but how it is possible to make an index file of this point?
> I want to include this index file as the ref_group in Umbrella Sampling.

Index files can't specify positions, only atoms.  In this case, you don't even 
need a special index group - just use the membrane.  The pull code uses the COM 
of the selected group, so if you specify your membrane, mdrun knows to use its COM.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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