[gmx-users] COM group of Membrane and Protein simulation

Justin Lemkul jalemkul at vt.edu
Fri Dec 2 13:51:04 CET 2016

On 12/1/16 9:17 PM, Mijiddorj Batsaikhan wrote:
> Dear gmx_users,
> I started simulation that a peptide on membrane. My peptide locates on the
> membrane surface. I have two questions relating to the simulation.
> (1)
> When I start the simulation, I chose COM groups separately. Is this choice
> okay? or May I need to chose COM group inseparately?

Your description is ambiguous; please post the actual .mdp contents.

> (2)
> During the simulation peptide is moving the edge of membrane. How can I
> shift the peptide to the central section of the membrane? Can I use
> -nojump, -center options of trjconv tool?

Yes - try it and see.  Also relevant is -fit transxy.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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