VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Apr 04 2012 - 09:13:37 CDT

On Wed, Apr 4, 2012 at 9:16 AM, Papan S <spapan2012_at_gmail.com> wrote:
> Dear all,
>
> For calculation of transport coefficients (unlike say, the RDF), it is
> advisable to not adapt the minimum image convention while calculating
> differences in position. However, say, one is interested in transport
> properties of water on a biomolecular surface (say a protein). Since the
> water on the surface will diffuse out, should not one wrap up the simulation
> trajectories (ie. use min. image) to calculate transport properties? Some
> advice is very much appreciated...

if you want to know the distance an atom (or molecule) has traveled,
you need to unwrap its trajectory, how would it work any other way?
with a surface, you don't have/need periodic boundaries in all three
directions, so you don't need to unwrap in the non-periodic dimension.
yet if your surface is not permeable, atoms won't travel across boundaries
in any case. so where is the problem?

axel.

>
> Thank you.
> -PapanS 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.