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.
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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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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