VMD-L Mailing List

From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Mon Aug 15 2011 - 02:43:51 CDT

Hi!

On 08/12/2011 05:19 PM, Thomas Evangelidis wrote:
> I want to select waters within a radius from my protein including
> those in periodic cells. The "pbwithin" macro selects waters from
> the periodic cells but does not wrap the protein that is near the
> boundaries or sticks out of the unit cell. Is there any effective
> way to automatically wrap my protein with period waters and iterate
> over all frames without manual intervention?

To wrap the atoms into the central unitcell, you can use the plugin pbctools

  http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

> Alternatively is there any way to know from which periodic cell the
> waters come from in order to make the respective translations?

Not that I know of.

Olaf 

-- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607