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

Justin Lemkul jalemkul at vt.edu
Tue Jul 16 13:46:47 CEST 2013

On 7/16/13 7:41 AM, Shima Arasteh wrote:
> 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?

Like everything in Gromacs, these are just group names.  You can use either 
default groups 
(http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups) or 
groups of your own creation.  The names specified must match either a default 
group name or a group name found in an index file.

See my umbrella sampling tutorial for examples.



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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