[gmx-users] Centering the system

[Justin Lemkul]

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

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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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