[gmx-users] Regarding membrane construction

Justin Lemkul 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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