[gmx-users] Problem - How to center a protein in a CG simulation
jalemkul at vt.edu
Tue Nov 11 00:45:35 CET 2014
On 11/10/14 10:01 AM, Carlos Navarro Retamal wrote:
> if there is not a way to do this at this moment (after the simulation) is there a way to apply a restraint to maintain fix the protein in the middle of the POPC bilayer (other than elastic network) during the MD simulation in order to avoid this problem?
I don't know why the -center option isn't working. That's precisely what it
does. Other things to try:
1. Often I find that PBC routines do not work well when dealing with a single
coordinate file. Processing the trajectory, then extracting the frame(s) of
interest works all the time.
2. Try the -fit transxy option of trjconv. It's designed for interfacial and
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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