[gmx-users] Regarding membrane construction
venkat4bt at gmail.com
Tue Jun 10 07:13:32 CEST 2014
I have used
editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro
to set the box.
genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro
Am I missing something here???
On Tue, Jun 10, 2014 at 2:51 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 6/9/14, 9:08 AM, Venkat Reddy wrote:
>> Dear Justin,
>> I have tried the command
>> genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro
>> but it got hanged. Is there something wrong with the command?
> I wouldn't expect a hang as long as the box is set to appropriate
> dimensions. The new box for the protein shouldn't be substantially larger
> than the membrane itself.
> 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
With Best Wishes
Venkat Reddy Chirasani
Laboratory of Computational Biophysics
Department of Biotechnology
More information about the gromacs.org_gmx-users