[gmx-users] Regarding membrane construction

[Venkat Reddy]

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???


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
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036