Nice Jason,
BTW, a typo in first link, "In this tutorial ... calculate normal modes for
entropy calcalations."
Cheers,
Alan
On Mon, May 24, 2010 at 23:53, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> My co-authors and I are pleased to announce the release of an update to
> MMPBSA.py. This is a significant update with many improvements and
> additions. I will briefly describe the improvements and additions, though
> they can be found in more detail in the RELEASE_NOTES.txt included with the
> new source code.
>
> Improvements and additions:
> - Normal mode calculations are done completely within a nab program
> - MPI has been implemented directly in python script, improving
> parallelization
> - Decomposition analysis (both per-residue and pairwise) implemented
> - Ability to rewrite outputs without re-doing calculations
> - More extensive test suite
> - Improved error catching and messages
> - Fixed many bugs in infrequently tested calculations
>
> This version, last updated around 5/21/2010, is even more recent than the
> version released recently with Amber11, so we encourage people that plan to
> use this script to upgrade to the new version. Old input files should
> continue to work except for the two changes mentioned below. All common
> calculations are discussed in detail in the tutorial for MMPBSA.py (
> ambermd.org/tutorials/advanced/tutorial3/py_script/index.htm). The source
> code can be obtained along with the installation instructions on this site
> (
> ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm).
>
> Changes:
> - initial_traj variable was changed to strip_mdcrd (more informative
> name). See manual.
> - mpi_cmd and nproc were removed as variables due to new MPI
> implementation
>
> Thanks!
> Jason, Dwight, and Bill
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Tue May 25 2010 - 00:00:05 PDT
