[gmx-users] Question regarding lipid bilayer pore formation

Justin Lemkul jalemkul at vt.edu
Wed Mar 8 14:09:07 CET 2017

On 3/8/17 8:05 AM, ali.khourshaei71 at student.sharif.edu wrote:
> Dear Gromacs users,
> Based on the previous published papers, I know that a 200bar pressure
> causes the lipid bilayer to rupture. Therefore I exerted a 200bar
> equibiaxially to my system and after a while it gave the following
> error:
> One of the box vectors has become shorter than twice the cut-off length
> or box_yy-|box_zy| or box_zz has become smaller than the cut-off
> Does it mean the same? Also Can I interpret this issue as pore
> formation?

A fatal error means the model physics broke down.  Whatever you did destroyed 
the system; it wasn't successful.



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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