Jmol users,
Thanks to Tim Vandermeersch and Geoff Hutchison for their generous contribution
of code and programming assistance, Jmol 11.5.21 adds real-time minimization.
That's a major step for Jmol.
I know we aren't in the business of doing calculations, but this is an area
that could significantly impact Jmol's visualization capability as well. I'll
let others discuss what this might be useful for. Suffice it to say several
people have asked for it.
An example script is shown here:
load caffeine.xyz
select connected(2) or connected(3) or oxygen and connected(1)
connect aromatic modify
calculate aromatic
set measurementunits pm
measure {_O}[1] {_O}[2]
color measure red
minimizationSteps = 80
minimizationRefresh = true
minimizationCriterion = 0.001
minimize
This says, "Load caffeine, make the appropriate atoms aromatic and display the
proper double bond/single bond picture, mark the distance between the two
oxygens atoms, and run a minimization."
The next thing you will see is the model jittering (because we asked for
minimizationRefresh=true) as it minimizes for up to 80 steps or until the
difference in energy between the last two energies is less that 0.001 kJ/mol.
The coordinates will be changed a bit, and the measurement line between the two
oxygens will be updated.
The minimization is done using the Universal Force Field, a molecular mechanics
minimization method described at
A. K. Rappé,
C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skiff,
/J. Am. Chem. Soc. /114, *10024* (1992).
What I'm hoping for is a discussion now of what you need from me to make Jmol
minimization do what you need it to do.
You can test it out at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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