VMD-L Mailing List

From: Bjørnar Jensen (bje076_at_ift.uib.no)
Date: Fri Feb 15 2013 - 04:09:18 CST

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
-----------------------------------------------------------------------------

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