[gmx-users] problem with membrane simulation
jalemkul at vt.edu
Fri Jun 6 20:07:46 CEST 2014
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 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
More information about the gromacs.org_gmx-users