VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Sep 06 2013 - 05:09:23 CDT

On Fri, Sep 6, 2013 at 10:52 AM, Oliver Stenning
<s3253462_at_student.rmit.edu.au> wrote:
> Hello,
>
> I have been searching for the formula in which determines if two atoms are to be bonded together in VMD using the auto bond feature.
> What is this formula?

from BondSearch.C:

          if (radii) { // Do atom-specific distance check
            float cut = 0.6f * (radii[ind1] + radii[ind2]);
            if (ds2 > cut*cut)
              continue;
          }

so a bond is assumed, if the distance between two atoms is smaller
than 0.6 times the sum of the two atom radii.

axel.

>
> Regards,
> Oliver 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.