FEP and restraints

From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Tue Mar 23 2004 - 13:45:32 CST

Dear Users,

I carry out FEP calculations while restraining some
atoms. Looking at the FEP output it seems that only
the VDW and ELEC terms go into calculating the
free energies. So I assume that my restraining potentials
are not included in the hamiltonian when calculating the
exponential averages.

Is this correct?

Michael Grabe, Ph.D.
Post-doctoral Fellow
Howard Hughes Medical Institute
University of California, San Francisco
533 Parnassus Ave.
San Francisco, CA 94143
tel: ++ 415.476.6585

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