[gmx-users] Centering the system
shima_arasteh2001 at yahoo.com
Thu Oct 17 20:09:06 CEST 2013
I used -fit or boxcenter or trans or .. any other thing which I though to solve my problem, but did not work. Would you give me a hint pleaaasssee?
Thanks a lot.
On Wednesday, October 16, 2013 4:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
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 A. Lemkul, Ph.D.
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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