VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Dec 29 2008 - 09:31:59 CST

That only applies when using two separate selections. It should be
fine with just one.

On Dec 18, 2008, at 5:59 PM, Harindar Keer wrote:

> Dear all,
>
> I am somewhat confused by the known issue listed in the VMD guide
> (Known Issue: The output of hbonds cannot be considered 100%
> accurate if the donor and acceptor selection share a common set of
> atoms)
>
> I am evaluating the number of h-bonds in a selection of water
> molecules itself. I am using following command
>
> measure hbonds $cutoff $angle $selection
>
> I would like to confirm whether the list of h-bonds obtained is
> 100% accurate. I would sincerely appreciate if some one can clarify
> this issue for me. Many thanks.
>
> Warm regards,
> Harindar Keer