[gmx-users] Vacuum disappear after NPT equilibration?

Justin Lemkul jalemkul at vt.edu
Sat Jan 18 21:18:00 CET 2014

On 1/18/14, 3:05 PM, Guangwei Jiang wrote:
> Hi, Mark,
> I hope to introduce the ions into two water compartments above and below the lipid bilayers. But with the vacuum, I can block the ions flowing into the other side. This may overcome the case from periodic boundary condition.
> But I need to have such a stable structure with vacuum. Do you have any suggestions towards the equilibration?

Using "pbc = xy" in conjunction with walls (and other necessary settings listed 
in the manual) circumvents this problem.  Or, as I suggested before, setting a 
zero compressibility in the z-dimension should be adequate.



Justin A. Lemkul, Ph.D.
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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