[gmx-users] BAR gives different result than TI
michael.shirts at virginia.edu
Sat Jul 7 21:46:49 CEST 2012
The implementation of BAR in gromacs is pretty hard for me to follow
because of how everything is stored noncompactly in the histogram. In
4.6, both can be computed from the same dhdl.xvg file, so it might be
easier to track down possible bugs.
On Fri, Jun 29, 2012 at 2:24 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> we've been trying to do free energy calculations for solvation of two small
> molecules in water, n-butylamine (NBA) and diethyl-ether (DEE). For one of
> them the result with BAR (using Justin's tutorial) is significantly
> different from TI:
> BAR TI Exper. (kJ/mol)
> NBA -11.1 -10.8 -17.9
> DEE -11.0 -1.8 -7.4
> Since for NBA the results are pretty close it seems that the protocol should
> be right, and the numbers seem to have converged pretty good as well.
> Any clues why these results could be so different?
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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