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
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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