[gmx-developers] Energy analysis

David van der Spoel spoel at xray.bmc.uu.se
Wed May 7 17:41:48 CEST 2014

On 2014-05-07 17:31, Shirts, Michael R. (mrs5pt) wrote:
>> - the free energy estimate code
> yes
>> or whether I can drop those?
> So I would vote for not dropping them.
OK, message taken.

> Berk, by using the free energy estimate code, do you mean g_bar, or the
> single pass free energy estimate described on page 274 (D.31) of the
> manual (Actually, looking at 4.5.6 of the manual).  Just to clarify.
This is what is implement in g_energy.
> Eventually, it seems like there should be one process (either single pass,
> or g_bar, but not both).  Actually, it would be best to put it in an MBAR
> context, but that's on me . . .
Some streamlining would be good. Is there any hope of getting the pymbar 
functionality into g_bar by the way? Just asking since my student did 
not manage to make pymbar work due to  !@#$%^&*() python.

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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