VMD-L Mailing List

From: Nicholas Musolino (musolino_at_mit.edu)
Date: Tue Apr 20 2010 - 11:27:39 CDT

On Apr 20, 2010, at 11:11 AM, yongpingzeng wrote:
> Dear VMD users:
> I encounter with the issue of handling periodic boundary conditions while detecting Hydrogen bonds for pure water. For instance, the command 'measure hbonds' is not aware of PBC, and will miss whatever bonds may extend across the edges of the periodic box.
> I dont know if the problem have been resolved? Could anyone like to give me some help?
>
> Best
> Yongping Zeng
> Yangzhou University

Thanks for searching the list archives before mailing. The post by John Stone that you copied is prescient, actually. If you search for "pbcwithin," you may find the functionality you're looking for. See this thread:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/11587.html

I think that by now the pbcwithin ability is included in the standard 1.8.7 distribution, but someone can correct me if I'm wrong.

Using that, you could engineer your own H-bond measurement script. Hope this helps!

Best regards,
Nicholas
---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino_at_mit.edu | 617-253-6675 | Room E19-528