[gmx-users] more free energy questions

David spoel at xray.bmc.uu.se
Tue Nov 11 22:15:01 CET 2003

On Tue, 2003-11-11 at 21:09, Ilya Chorny wrote:
> Hello,
> 	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
> simulations
Is it really tha crazy? It could be due to a particular conformation of
the balls.

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

> Ilya
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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