[gmx-users] problem with membrane simulation

[Justin Lemkul]

On 6/6/14, 7:22 AM, free882 at inwind.it wrote:
> hi all,
> I'm trying to do a simulation of a membrane protein in DPPC, with Gromacs4.6.
> I used gromos96 53a6 as forcefield. I'm following KALP15 tutorial of gromacs.
> I'm trying to orient protein in membrane but I can't with editconf because I
> don't know what parameters I had to use as center of mass.
> I've tried to move the membrane in the correct orientation with vmd but when I
> do the energy minimization, the membrane change position.
> how to fix it?

editconf is the proper tool to use to place the protein.  Leave the membrane 
alone; manipulate the protein's coordinates.  editconf provides all the options 
you need to align, translate, or rotate the protein.  Identifying the proper 
orientation can be challenging, but based on the composition of the 
transmembrane domain and its dimensions, it should be easy to construct a rough 
guess that should equilibrate and reorient as needed over time.

-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 601
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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