Proto_MD is a prototyping toolkit for multiscale MD.

Authors

Endre Somogyi, Andrew Abi Mansour

Institution

Indiana University, Bloomington

Prerequisites

• GromacsWrapper: https://github.com/CTCNano/GromacsWrapper
• MDAnalysis: https://code.google.com/p/mdanalysis
• Numpy: http://www.numpy.org
• Scipy: http://www.scipy.org
• OpenMPI: http://www.open-mpi.org or MPICH: https://www.mpich.org
• Gromacs: http://www.gromacs.org

protoMD has been tested with:

• Gromacs 4.6.x and 5.0.x
• MDAnalysis 1.0.0

Installation

Installation uses python's setuptools.

To install protoMD, simply run from the cmd line:

pip install proto_md

Testing Package

You need to have pytest installed:

pip install pytest

and then run from the proto_md src dir:

pytest -v

Working Example

A bash script that creates an input (hdf) file and runs a multiscale simulation is found in the sample dir.

To run it, simply execute from the terminal: bash run.mkconf

Source Code

• proto_md/config.py: handles configuration of proto_md environment variables and templates.
• proto_md/correlation.py: functions for computing correlation functions.
• proto_md/diffusion.py: functions for computing diffusion coefficients.
• proto_md/dynamics.py: functions to calculate dynamic properties of CG variables.
• proto_md/init.py: initializer for importing proto_md as a package
• proto_md/main.py: functions for arg parsing (when using proto_md as a program)
• proto_md/md.py: functions for setting up and performing md calculations.
• proto_md/system.py: functions for creating the System object, handling I/O, and calling MD functions
• proto_md/subsystems: contains modules specific to various coarse-graining methods
• proto_md/util: contains modules for reading and writng files to / from disk and hdf blobs
• proto_md/templates: contains GROMACS mdp config template files
• proto_md/integrators: contains modules for various multiscale integrators
• proto_md/fieldVars: C++ code for an (optional) subsystem based on continuum field variables

License

GPL v3