On 10/16/13 8:29 AM, Shima Arasteh wrote:
Dear gmx users,
I have a system consist of a lipid bilayer and a peptide. As the initial
configuration, the peptide is located in center of the x-y plane above lipid
bilayer. After running MD, the peptide shows interactions with the polar
groups. It's ok, but the peptide is near one edge of the x-y plane of the
bilayer. I' d like to know if there is any way to use the properties of the pbc
and see the peptide in center of the x-y plane while interacting with the
polar groups?
trjconv has a number of ways to deal with this. Please read trjconv -h.
-Justin
--
==================================================
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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