VMD-L Mailing List

From: Jevgenij Raskatov (jraskato_at_ucsc.edu)
Date: Wed Feb 25 2015 - 21:07:32 CST

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