[gmx-users] Membrane simulation npt problem

[Justin Lemkul]

On 1/15/16 12:56 PM, Marco Franzoi wrote:
> Good evening to everyone.
>
> I've an issue regarding a membrane simulation.
> I've downloaded an already equilibrated POPE/POPG membrane and, to test the
> system, I run an em, a 0.1 ns nvt and 1 ns npt simulation and everything
> was fine.
>
> Then, I've raised the cell lenght in the z direction and added a peptide,
> solvate, ionized and minimized. The next ntv step was also fine but, when I
> run the npt simulation, suddenly the cell broadens in xy directions and
> shrinks in z direction.
>
> What can be wrong with it?
>

How much do the box vectors change?  Some change is, of course, expected.

> My npt.mpd file is attached.
>

Please provide the text of the .mdp file; the mailing list does not accept 
attachments.

-Justin

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

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
http://mackerell.umaryland.edu/~jalemkul

==================================================