VMD-L Mailing List

From: Dave Schall (schalljd_at_gmail.com)
Date: Thu Feb 14 2013 - 13:52:07 CST

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