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

Justin Lemkul jalemkul at vt.edu
Tue Jul 16 13:09:57 CEST 2013

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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