[gmx-users] more free energy questions

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Tue Nov 11 21:10:01 CET 2003


	I ran a simulation to calculate the solvation free energy between soft
spheres where the potential energy is (v=kt(3/r)^12 and six of the same
spheres fused together at a distance of three angstroms. I ran the
simulation at constant NVT. My box contains about 4000 H2O molecules and
is 5 X 5 X 5 nm^3. The used ten windows used lambda values
(0,.1,.2,.3,.4,.5,.6,.7,.8,.9,10) starting with one ball at lmabda = 0
and ending up with 6 balls at lambda equals 1. I get a reasonable result
of about 97 kj/mole. Previous work has shown the solvation free energy
of one ball is about 20 kj/mol and I would expect six balls fused
together to be less. I then take the six ball and mutate them to to five
balls  using just one lambda value of .5. Doing this I get crazy results
(50-60 kj/mol). Any ideas what is going on? Any help would be greatly
appreciated. Statistical convergence tests were used for all the

P.S. I noticed in my first simulation that the value I got at lambda =
.5 was about the same as my overall result.

Ilya Chorny Ph.D.         Department of Pharmaceutical Chemistry
Postdoctoral Researcher   University of California-San Francisco
phone: (408)-887-8496     Genentech Hall 600 16th St Box 2240
fax: (415)502-1411        San Francisco, Ca, 94107
            email: ichorny at maxwell.ucsf.edu

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