PBCwrap: wrapping DCD files

From: Vani Krishna (vakri2002_at_yahoo.com)
Date: Mon Jun 28 2004 - 22:03:45 CDT


i tried using the script but there are some problems.

the coordinates in this case are wrapped such that
there are these weird bonds going across the box. if i
just run for a few steps in NAMD with 'wrapAll' turned
on, there is wrapping, but no weird bonds across the
box. I don't know what is the difference between the
two wrappings

any suggestions?

--- John Stone <johns_at_ks.uiuc.edu> wrote:
> Assuming you're using NAMD and you have the
> appropriate .xst files,
> then this script may do what you're asking for:
> John Stone
> vmd_at_ks.uiuc.edu

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