[gmx-users] pbc problem

Justin Lemkul jalemkul at vt.edu
Wed Oct 30 02:29:50 CET 2013

On 10/29/13 12:02 PM, shahab shariati wrote:
> Dear Mark
> Very thanks for your reply
>> To make this clear, center the trajectory on the water and watch the
>> time evolution in some visualization program.
> I did your suggestion (center the trajectory on the water). Again, drug
> molecule is in region (1)in some frames and is in region (4) in other
> frames.
> ----------------------------------------------------------------------------------
> Dear Justin
> Very thanks for your attention
>> As has already been stated several times, there is no problem at all.
>> The outcome is completely normal, and there are not discrete
>> regions (1) and (4).
>> It is a continuous block of water via PBC.  The molecule can freely
>> diffuse throughout it.
> If outcome is completely normal, Can I use this structure for pmf
> calculation. I want to calculate potential of mean force, delta G, as a
> function of the distance between the centers of mass of drug and the
> centers of mass of bilayer.

Given the inherent symmetry of the system, yes.



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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