VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Wed Apr 27 2005 - 10:01:50 CDT

On Wed, 27 Apr 2005, haider abbas wrote:

dear haider,

HA> Dear Axel and Eduard,
HA> thank you very much for your email. I am again writing
HA> in detail so that i could be able to completely remove
HA> the missing bond problem with your help.
HA> i am simulating pressure induced amorphization of
HA> alpha quartz by classical MD and with CPMD. the file
HA> created by classical MD run clearly shows 5,6,7..
HA> coordinated Si atom when it is visualized by "rasmol",
HA> which is confirmed by the previously published
HA> literature. When i visualised the same file with "vmd"
HA> it shows Si atom only four coordinated. I tried the
HA> same option (dynamic bond ) as told by you but when i
HA> increased Distance cutoff, first it start showing
HA> much oxygen-oxygen bond which is not expected and then
HA> it shows increased Si-Si bond. i dont understant what
HA> the value for cutoff should i use so that it may show

please don't get offended, but i do not consider using the
heuristics of a visualization program (in your case rasmol)
without actually knowing what they are a good measure for
what is a bond or not. i don't know what the conventions
in the case of Si-O bonds are, but, e.g., in the case of
water, the first minimum of the O-H pair-correlation function
would be a natural choice for the distance cutoff.

granted, your situation is (currently) handled badly, since
the VMD does not allow you to specify a different cutoff
for, say, Si-O and O-O bond with Dynamic Bonds. what might
work, however, would be the hack discussed earlier to
set the covalent radius of atoms (to determine radius for
the VDW representation).

HA> the same number of bonds between all atoms as it is
HA> shown by rasmol, Because the file created by CPMD are
HA> in XYZ format and can not be visualized by rasmol and

oh, yes you _can_ load xyz files into rasmol. try:

load xyz GEOMETRY.xyz

at the rasmol prompt. works nicely for me.
it sometimes helps to RTFM.

HA> there is much more option in vmd . Again the second
HA> problem is that the nearly all published paper shows
HA> the snapshots in sphere and lines format which is
HA> equivalent to "CPK" option of vmd. That is why i need
HA> the snapshot in CPK format which must also clearly
HA> show the all bonds between all atoms.

using selections and the vmd script interface you
can set the bonds to anything you like. if you would
send me an example geometry and the radii of the
first maximum and minimum of the Si-O radial distribution
function, i may be able to post an example vmd script
to do that.

to emulate a CPK rep, you can easily add a VDW rep
with a sphere radius of 0.2 on top of the dynamic
bonds. this is explained in the users guide, IIRC.

regards,
        axel.

HA> thanks
HA> please spend some time in my help
HA> yours sincerely
HA> Haider Abbas
HA>
HA>
HA>
HA> ________________________________________________________________________
HA> Yahoo! India Matrimony: Find your life partner online
HA> Go to: http://yahoo.shaadi.com/india-matrimony
HA>
HA> 

-- 
=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.