[gmx-users] Regarding membrane construction

[Justin Lemkul]

On 6/10/14, 1:12 AM, Venkat Reddy wrote:
> I have used
> editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro
> to set the box.
>
> Then
> genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro
> got hanged
>
>
> Am I missing something here???

Don't extend the z-dimension at this stage.  You want to expand the membrane 
laterally (along x and y, usually), so set the box vectors manually with 
editconf -box, not -d (though using -d can tell you what suitable vectors in x 
and y might be).  You can always increase the z-dimension, if you need to, later 
using editconf and then fill with water using genbox in a separate step.

-Justin

-- 
==================================================

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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