AMBER Archive (2003)

Subject: free energy in sander

From: Joseph Fernandez (joefern9999_at_yahoo.com)
Date: Thu Apr 10 2003 - 16:32:52 CDT

AMBER 7 manual mention that Sander could be used for
free energy calculations (using TI) for OH -> O-
process (since vdW parameter for H bonded to OH is
zero). Could this be used for NH4+ to NH3 if dummy
atom is defined with zero vdW? If so does klambda
have to be greater than 1?

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