On Mon, May 24, 2010 at 8:39 PM, Beroza, Paul <Paul.Beroza.elan.com> wrote:
>
> How do we obtain the new release of mmpbsa.py?
>
The source code is found in the second link provided in the release email:
source code can be obtained along with the installation instructions on
this site (ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm).
If you have any more questions, please feel free to ask.
Good luck!
Jason
> Thanks, Paul
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Jason Swails
> Sent: Monday, May 24, 2010 3:53 PM
> To: AMBER Mailing List
> Subject: [AMBER] MMPBSA.py update
>
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon May 24 2010 - 18:30:04 PDT
