AMBER Archive (2001)

Subject: intprt option in Thermodynamics integration

From: Marcela Madrid (mmadrid_at_psc.edu)
Date: Wed Jan 10 2001 - 19:51:22 CST

Hi

I am repeating the example from Gibbs of charging a sodium ion
in a box of water. "Intprt" determines which
energies contribute to the free energy calculation. I am setting
Intprt=0,
which means no
intra-perturbed group energies are accumulated. I would have
expected in this case to get the same results regarding of
the value of intrprt, since the perturbed group is only one ion, as
shown
in the file PATNRG:

Group legend: (Group #:atom #:res #:atom_name)
    1: 1: 1:NA //
 ***> Total number of groups defined = 1

However, the free energy difference when intprt=0 is exactly zero. Why
are the interactions between the ion and the solvent not taken into
account
in this case?

thanks, Marcela