[gmx-users] Centering the system

Shima Arasteh 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.
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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