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Joined: Mar 2004
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gkamath Offline OP
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Hi ,

I am not clear about this. Is the electrostatic charges scaled for intramolecular interactions in Charmm force field. How does one go about changing the sigma and epsilon once the charges for the interaction sites are determined. Is it trial and error (to reproduce properties of substances) or is there some optimization done!

Thanks,

Ganesh

Last edited by alex; 06/11/04 11:58 AM.
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Ganesh,

Typically you should just transfer LJ parameters directly from known
parameters based on analogy to the atoms in your new molecule. Such direct transfer is typically adequate unless you have a very novel atom type or are working with an atom that has not been previously parameterized. LJ parameter optimization is a difficult and tedious process; you can go to my web page for more information if you want to learn more.

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

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