VMD-L Mailing List

From: zhenlong li (zxl1000_at_gmail.com)
Date: Fri Jul 27 2007 - 13:00:54 CDT

Dear all,
As default, atoms crossing the periodical boundaries are wrapped in DCD
file, this causes problem when only part of a molecule crosses the
boundary. Is there any easy way to modify the DCD file, so that only whole
molecules crossing the boundaries will be wrapped? I've tried the unwrap
command in the pbctools plugin. But the trajectory is still a destroyed one
since the way of unwrapping is not unique. Thanks in advance!

best,
Zhenlong