[gmx-users] Re: problem in g_membed

Justin Lemkul jalemkul at vt.edu
Mon Jul 8 11:40:20 CEST 2013

On 7/7/13 10:52 PM, pavithrakb wrote:
> Dear Sir,
> Thanks so much..
> now what's the solution? Should I increase the box size?

Yes.  If the protein protrudes "out" of the central image, then you will have an 
unstable system due to atomic overlap as well as violations of the minimum image 

> Already I have centered the protein and fixed the POPE membrane size.
> Can you tell me how to increase the box size? or is there any other
> solution?

If you need more space in the x-y plane, use genconf to replicate the membrane 
patch appropriately.  If x-y is sufficient and only z is the problem, use 
editconf to adjust the box size and (if desired) the location of the 
membrane-protein complex  and then solvate with genbox to fill the newly 
introduced void.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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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