[gmx-users] PBC problem in bilayer system

Justin Lemkul jalemkul at vt.edu
Sun Sep 14 19:12:44 CEST 2014

On 9/14/14 10:29 AM, shahab shariati wrote:
> Dear Justin
> Based on your previous reply, I used following:
> trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc  -pbc mol –trans 0 0 7
> When I see **.xtc using vmd, unfortunately, problem was not solved.
> Please see the following link:
> https://www.dropbox.com/s/345o7lvc9z4jwln/figure%204.TIF?dl=0

 From that picture, it is clear that it is simply impossible to gather all of 
the drug molecules on one side of the membrane.  They have bound to both sides; 
there's no changing that since it's not an imaging issue.  If some were bound 
and others were simultaneously still free in the water layer, it could be done. 
  In this case, it cannot.



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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