[gmx-users] BAR / g_bar problems

Michael Shirts mrshirts at gmail.com
Fri Aug 24 17:09:13 CEST 2012

Hi, David-

Perhaps we can work with you to compare the internal g_bar
implementation with our external BAR and MBAR implementation run from
the .dhdl.xvg data output in 4.6.  It would probably be easier to run
these calculations after the optimization updates are added in the
next few days(?), but we can plan now.  Note that withe errors this
big, 100-200 ps should be enough to see what's going on, so it can be
done rapidly.  Drop me a line off the list to figure out details?


On Fri, Aug 24, 2012 at 9:22 AM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> Hi,
> we have terrible problems to get reasonable results from BAR free energy
> calculations. We basically follow Justin's tutorial for solvation of
> methanol, ethanol, diethyl-ether and neopentane in water using OPLS but get
> very strange results. The free energy curves are here:
> http://folding.bmc.uu.se/images/koko.jpg
> Molecule  Energy Exper
> Methanol     -8    -21
> Ethanol      -9    -21
> Diethylether -11    -7
> Neopentane   -10   +11
> any clue?
> --
> 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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