openmm 0.2

OpenMM command line script

This program sets up and runs an OpenMM simulation in a user-friendly way. It is roughly equivalent to to grompp/mdrun in Gromacs, dynamic in Tinker, and pmemd in Amber.

To install this package, run python setup.py install. The only dependencies are python and OpenMM.

For the short help, run openmm -h. To get help on all available options, run openmm –help-all.

You need to provide coordinates and specify a force field. Coordinates may come from a .pdb file. Built-in protein force fields and water models are shown in the help text, and you may add your own OpenMM force field XML files. Alternatively, you may provide AMBER inpcrd/prmtop files.

You may provide simulation options through the command line; all options are given in the help text. Every time this program executes, it makes a ‘configuration file’ which you may use as input for future runs using the –config argument. The command line options take priority over those in the configuration file. This provides a convenient way to customize your default options.

Some nice features include:

1) Extensive validation of options and checking dependencies / conflicts between options.

2) Reports your simulation progress, including speed in ns/day and time left.

3) You may use units from simtk.unit on the command line when specifying options with physical units.

4. Suggestions are provided for typos on the command line.

5) Restart files that contain state information (coordinates, velocities, and unit cell vectors) from the previous run.

This program is provided as an option for users to use OpenMM without needing to write a Python script. To take advantage of the full flexibility of OpenMM as a domain-specific language for molecular dynamics simulation, check out the OpenMM Script Builder located at http://builder.openmm.org.