VMD-L Mailing List

From: yongpingzeng (yongpingzeng_at_163.com)
Date: Tue Apr 20 2010 - 10:11:38 CDT

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.
Jonh Stone have given some hints:
In the post in 2005
> existing VMD functions that do:
> - 'within' and 'exwithin' atom selections
> - 'measure contacts'
> - 'measure hbonds'
> - automatic bond search (allow bonds across PBC cell boundaries)
> - draw bond components of the Bonds, CPK, and Licorice representations
> - draw dynamic bonds representation
>
> Adding PBC-awareness to the drawing code is the most risky in terms
> of hurting performance, but this may be something that could be dealt with
> by adding a checkbox so that VMD only spends effort checking for this when
> the user actually needs it.
>
> Before embarking on implementing all of this, it wvmd-l_at_ks.uiuc.eduould be nice to know
> which of these users would find most beneficial. We could work on the
> most-wanted features first...
>
> John Stone

I dont know if the problem have been resolved? Could anyone like to give me some help?
 
Best
Yongping Zeng
Yangzhou University