[gmx-users] Regarding membrane construction
venkat4bt at gmail.com
Wed Jun 11 12:25:41 CEST 2014
I am following membrane-protein tutorial to construct my system. During
equilibration and production MD, I am receiving the following NOTES.
NOTE 1 [file md.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file md.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
I have downloaded the mdp files from tutorial. Is it ok if I omit these
notes and carry the production run?
On Tue, Jun 10, 2014 at 5:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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.
>> 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 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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With Best Wishes
Venkat Reddy Chirasani
Laboratory of Computational Biophysics
Department of Biotechnology
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