VMD-L Mailing List

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Wed May 09 2007 - 01:37:14 CDT

Hi,

I have been using DL_POLY version 3 to create trajectories. When I
visualize, it appears that all of the coordinates are wrapped with the
periodic boundary conditions. So the coordinates of some atoms are not kept
with the molecule (as pbcwrap does with NAMD dcd files). So when bonds are
drawn they are somtimes extended across the box! Is there a way to unwrap
these coordinates? I tried using pbcunwrap from below, but I didn't have
much luck.

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8967.html

Is there a DL_POLY expert in the list that has already found a way around
this?

Thanks.

Josh