VMD-L Mailing List

From: M K (mahyar.karimi20_at_gmail.com)
Date: Wed Feb 25 2015 - 21:43:06 CST

Yes, because you have used periodic boundary conditions.

BTW, you can see the system with its periodic images using the following
option:

Graphics > Representations > Periodic

add -x, +x, -y, +y, -z, or +z images based on the periodic boundary
conditions.

On Thu, Feb 26, 2015 at 2:07 PM, Jevgenij Raskatov <jraskato_at_ucsc.edu>
wrote:

> Dear all,
>
>
> I am running simulations using periodic boundary condition. Sometimes I
> will see the molecule partially diffuse out of the box and enter from the
> other side - can I assume that in those instances the solvation is fully
> accounted for due to periodicity and the relevant waters are simply in
> neighboring boxes that are not shown?
>
> Thanks
>
> Jevgenij
>
> --
> Dr. Jevgenij A. Raskatov
> Assistant Professor in Chemistry and Biochemistry
>
> Tel.: +1-831-459-2978
>
> Department of Chemistry and Biochemistry
> Physical Science Building 356
> 1156 High Street
> Santa Cruz, CA
> 95064 USA
>