Re: NAMD - wrap atoms, not center of mass

From: Josh Vermaas (
Date: Fri Oct 16 2015 - 10:48:35 CDT

Hi Stano,
There is not a documented way of doing this, an usually it isn't
something you'd want to do, since your molecules will get split across
periodic boundaries, and it looks hideous for many bond-based
visualizations. If you want to do this, trajectory postprocessing in VMD
or other tools will let you do this manually.
-Josh Vermaas

On 10/16/2015 10:20 AM, Stanislav Ċ imko wrote:
> Dear NAMD users,
> I would like to ask you if it is possible (and if yes than how) to wrap
> atoms immediately as they cross box boundaries - do not wait till
> center of mass crosses the boundaries.
> I tried wrapAll as well as wrapNearest and their combination, however,
> they seem to me to work the same way.
> Thank you.
> stano simko.

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