From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 21 2012 - 11:29:49 CDT

Hi,
  The distance-based bond search heuristic uses a fairly simple test.

Assuming your atoms have radii assigned, it generates bonds for pairs
that are less than 0.6 * (r1 + r2):
         if (radii) { // Do atom-specific distance check
            float cut = 0.6f * (radii[ind1] + radii[ind2]);
            if (ds2 > cut*cut)
              continue;
         }

Those candidate bonds are subsequently filtered according to other
tests that prevent bonds that shouldn't exist even though the distance
criteria has been met.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 19, 2012 at 09:45:34AM -0400, Zhuyi Xue wrote:
> Hi, there,
>
> What is the cutoff vmd use to determine the presence of a bond between
> two atoms when I open a gro file?
>
> Thanks!
>
> Regards,
> Zhuyi

-- 
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