VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Fri Jul 09 2004 - 12:11:46 CDT

>>> "PD" == Peter Deák <deak_at_phys.upb.de> writes:

PD> Dear All (especially dear Deveopers),

PD> My group has recently started to use VMD - on all three platforms - and
PD> we find it wonderful. We are a group of solid state physicists,
PD> interested in defects in crystals. Finding localized states in the
PD> haystack has always been difficult but VMD makes wonders. (I feel like
PD> Columbus could have if - at the end of his life - he had been offerd a
PD> flight to America.)

PD> There is just one tiny wish we have: could someone tell us, how could
PD> we make VMD recognize Si as silicon and not sulphur, and make bonds
PD> between Si atoms 2.35 A apart.

PD> Then we could go out and show our beautiful VMD pictures to the world!

dear peter,

the easiest way is probably to not use a CPK representation
but a VDW representation _and_ a Dynamics Bonds representation
where you can set the bond distance manually.

if this is not feasable, you could also create a psf file
(which would require that you write a program to create it,
as most available tools are geared towards biomolecules).

finally, you can also set bonds manually from the vmd command
prompt (or a script) via selections and the 'getbonds/setbonds'
subcommands (which is probably quite tricky in your case).

regards,
        axel.

PD> Thanks!!!

PD> Peter

PD> _______________________________________
PD> Prof. Dr. Peter Deák
PD> Head of the Surface Physics Laboratory
PD> Department of Atomic Physics
PD> Budapest University of Technology & Economics
PD> Budafoki ut 8, H-1111 Budapest, Hungary
PD> Phone: [36]-(1)-463-4207 Fax: [36]-(1)-463-4357
PD> e-mail: p.deak_at_eik.bme.hu
PD> http://qchem52.fat.bme.hu 

--
=======================================================================
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.