VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Jul 27 2007 - 16:48:26 CDT

If you're using NAMD then entire fragments are wrapped, so you should
never have bonds crossing the cell unless they started out that way in
your input coordinates.

-Jim

On Fri, 27 Jul 2007, zhenlong li wrote:

> 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
>