[gmx-users] Regarding error after equilibration of protein in membrane using g_membed

Justin Lemkul jalemkul at vt.edu
Thu Feb 20 22:49:31 CET 2014

On 2/20/14, 9:47 AM, shalini.s at iitg.ernet.in wrote:
> I am attaching the membedded.gro which was created using g_membed...Kindly
> suggest..

The box is much too small in the z-direction.  Your protein is overlapping with 
itself, leading to the crash.  You may need a larger membrane patch, but you 
definitely need to increase the box size along z.



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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