VMD-L Mailing List

From: Papan S (spapan2012_at_gmail.com)
Date: Wed Apr 04 2012 - 23:06:18 CDT

Thanks. By a "surface", I did not mean a flat surface, but an unevenly
curved surface, such as a protein has. If I am interested in the movement
of waters within a few Å of the rough protein surface, I would need min.
image to locate them anyways. How is transport taken care of, for this
layer?

On Wed, Apr 4, 2012 at 7:43 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>