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 PyOpenMM: Python utilities for OpenMM
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URL: https://simtk.org/home/pyopenmm

PyOpenMM is a collection of utilities for use with OpenMM, which is a
library that provides tools for performing GPU accelerated molecular
simulations.  See the OpenMM project home page for more details:
https://simtk.org/home/openmm

To use PyOpenMM, you must first install OpenMM, including the Python
API wrappers.  Consult the OpenMM User Guide for instructions on how
to do this.


INTENDED AUDIENCE:
This README is intended for people who downloaded the PyOpenMM package
from the simtk.org website.


INSTALL
First unzip the package, change to the new directory, and run
the following two commands from a command line:
 python setup.py build
 python setup.py install


TEST INSTALL
Next run the following test to see if the install worked (it
should report "OK"):
 python test/test_openmm.py
This should return "OK".


FEATURES
PyOpenMM includes the following features:

1. A collection of examples and test cases for OpenMM written
in Python
2. Modules for reading and writing various types of files, including
PDB files and AMBER prmtop and crd files
3. A script (zander.py) for running simulations based on AMBER input
files, using an interface almost identical to Sander
4. A module for performing replica-exchange simulations
5. A class for representing three component vectors


PYOPENMM USAGE EXAMPLES
Once you have tested the installation, switch to the example
directory (cd examples), and try running one of the simulations.
For example, run the argon simulation by changing to the examples/argon
directory and typing the following:
 python runArgon.py argon.pdb

If all goes well, this will produce a PDB formatted file called argon.pdb,
which can be visualized using a program such as VMD.


FEEDBACK
Please address all comments, criticisms, suggestions, etc to one of us:
Mark Friedrichs at friedrim@stanford.edu
Peter Eastman at cmbruns@stanford.edu 
Randy Radmer at radmer@stanford.edu