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
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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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