[gmx-users] Regarding membrane construction

[Venkat Reddy]

Dear Justin,
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.
>>
>> 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
>
> ==================================================
> --
> 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
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036