From: Axel Kohlmeyer (
Date: Fri Feb 15 2013 - 05:20:31 CST

On Fri, Feb 15, 2013 at 11:09 AM, Bjørnar Jensen <> wrote:
> Hello Dave,
> I can't think of any smart selections that can do this for you. But there is
> a work around. It requires some effort, though.
> Via the "atomselect" command, you can get and set bond lists. This enables
> you to manually (via a script) assign the
> correct bonds, thus avoiding this whole problem.
> A pseudo-code for the script would be something like:
> -----------------------------------------------------------------------------
> Select everything
> Store bond list
> For each list in bond list grab the index of each atom.
> Check elements
> Calculate distances
> Add/remove bond depending on element/distance
> Update bond list

there is yet another way, that may be a compromise of convenience and
flexibility. you can tweak the normal bond guessing algorithm of VMD
by changing the atomic radii and then use "mol bondsrecalc top".
setting a larger atom radius will be equivalent of setting a larger
dynamic bond cutoff. the cutoff for individual bonds is computed via
mixing (i think geometric, but not 100% sure).


p.s.: i should probably also point out, that the topotools plugin
makes the "lets compute bonds explicitly" approach much easier, as it
has convenience functions to read and write bonds as a single list of
bonds (and not a list of neighbors for each atom).

> -----------------------------------------------------------------------------
> If the bonds changes during the simulation you'll need something slightly
> more advanced, which
> reads in a list of bonds for each frame (or calculates on the fly along the
> lines above). I did this two
> years ago for use with ReaxFF, which drops a bond list.
> Best regards,
> Bjørnar Jensen.
> On 2013-02-14 20:52, Dave Schall wrote:
>> Hello VMD users,
>> I have generated an amorphous silicon carbide structure using a bond order
>> potential and need some help visualizing it. It has 3 types of bonds: SiSi,
>> SiC, and CC. Drawing the SiC bonds is a bit of a trick. I use the dynamic
>> bonds representation and by using appropriate selections and adjusting the
>> distance cut off I can draw C-C and Si-Si bonds that look reasonable. The
>> problem is when I try to draw the SiC bonds. The C-C cut off is around 1.6
>> which picks up all the C-C bonds. To get the SiC bonds I need to increase
>> the cut off to about 2.0. This sometimes causes over bonding between C-C
>> (between 2nd neighbors and such).
>> Logically, I need to do a selection that only draws bonds only between C
>> neighbors of Si and vice versa to exclude C-C from the representation. Is
>> this possible with in VMD or is there a work around?
>> Thanks,
>> Dave
>> --
>> J. David Schall, Assistant Professor
>> Dept. of Mechanical Engineering, Oakland University
>> 130 DHE, Rochester, MI 48309
>> 248-370-2870

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.