[gmx-developers] Energy analysis

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Wed May 7 18:00:35 CEST 2014

> Some streamlining would be good. Is there any hope of getting the pymbar
> functionality into g_bar by the way?

I very much want to.  It's just a question of priority ordering.  Gromacs
priorities here (when I can make time for it!) are: 1) deep validation for
4.6 and 5.0, 2) getting the inner loop cleaned up for 5.1 and 3)
implementing a MC barostat.  MBAR and bar integration is probably 4.

> Just asking since my student did
> not manage to make pymbar work due to  !@#$%^&*() python.

Have him shoot an email my way and we can try to resolve the issues in the
mean time.  We've reconfigured the setup scripts and it should be much
easier to get working: https://github.com/choderalab/pymbar

>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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