FYI,
sorry for the duplicate to those who are subscribed to jmol-users...
Egon
---------- Forwarded message ----------
From: Bob Hanson <[EMAIL PROTECTED]>
Date: Thu, Mar 27, 2008 at 4:36 AM
Subject: [Jmol-users] Jmol 11.5.21 and minimization
To: [EMAIL PROTECTED], Miguel
<[EMAIL PROTECTED]>, Tim Vandermeersch
<[EMAIL PROTECTED]>, Geoffrey Hutchison
<[EMAIL PROTECTED]>
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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