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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Received on Mon May 24 2010 - 16:00:04 PDT
