[gmx-users] Regarding membrane construction
jalemkul at vt.edu
Mon Jun 9 14:00:39 CEST 2014
On 6/9/14, 3:22 AM, 陈功 wrote:
> Dear Venkat, I guess there are some other methods to generate new lipid
> bilayer construct by using genbox -cp your_membrane_protein -ci lipid_monomer
> -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o
> new_conf.gro or using editconf & cat ...Another way, you can try the script
> packmol. Be more patient. haha, I m also a new gmx user. Good luck, chen
Packmol is a good choice, but the approach above with genbox likely won't work.
It will produce a random insertion of lipids. The simplest way within Gromacs
to create a membrane of sufficient size is to place the protein in a suitably
sized box (with editconf) and then
genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro
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
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