[gmx-users] Problem - How to center a protein in a CG simulation

[Justin Lemkul]

On 11/10/14 10:01 AM, Carlos Navarro Retamal wrote:
> nobody?
> 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 
membrane systems.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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