VMD-L Mailing List

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Fri Aug 12 2011 - 10:19:47 CDT

Deal all,

I want to select waters within a radius from my protein including those in
periodic cells. The "pbwithin" macro selects waters from the periodic cells
but does not wrap the protein that is near the boundaries or sticks out of
the unit cell. Is there any effective way to automatically wrap my protein
with period waters and iterate over all frames without manual intervention?
Alternatively is there any way to know from which periodic cell the waters
come from in order to make the respective translations?

I would greatly appreciate any advice.
Thomas