[gmx-users] lipid membrane study and the increase in z dimension on dppc128.gro

Justin Lemkul jalemkul at vt.edu
Sat Oct 18 12:15:24 CEST 2014

On 10/18/14 2:26 AM, rama david wrote:
> Dear Justin,
>           I added the water as per your instruction and following the
> instruction from
> http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
>   I change the box size by editconf and  vdwradii.dat  files carbon radii to
> 0.45.
> I added the water with the genbox command.
>         I found that most water molecule are up to the N4, some are up to
> the Phosphate
> and few may be up to the 013, and 016. but no one is bellow this.
> Is this behaviour is right ???  or should I need also the script
> keepbyz.py to run on the system??
> I not get the any warning while Energy minimization,  NVT, NPT and MD  (
> that
>   mean system was not unstable and blown away)
> I am looking forward for suggestions

I don't know what suggestion you need.  Everything worked as expected.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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