Subject: Free energy calculations

From: "Charles R. Watts" <[email-masked]>
Date: Thu, 2 Nov 2000 06:29:11 -0600 (CST)

Dear CCL:
	I have used molecular dynamics to sample the conformational space
of a peptide in solution.  The sampled conformations were then clustered
into separate families of related conformations based on a pairwise
comparison of the RMSD of all conformations.  I would like to perform a
free energy analysis that compares the separate families of conformations,
hopefully in such a way that the solute and solvent terms could be
analyzed separately.for simplicities sake I would like to do this using a
representative conformation from each separate family.what would be the
most appropriate, valid method and would a free energy perturbation
calculate that mutates on conformation to the other be a valid choice?
Your opinions would be greatly appreciated.

Regards,

Charles R. Watts, M.D., Ph.D.         ************************************
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