From: Bob H. <ha...@st...> - 2008-03-27 03:36:13
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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 |