AdaptiveMasterMSM
AdaptiveMasterMSM is a Python package for doing adaptive sampling by employing Markov State Models (MSM) interacting with MasterMSM software and molecular dynamics simulations through GROMACS. This package will allow you to:
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Do adaptive sampling simulations
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Employ different scoring functions: 'counts' and 'probabilities'
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User MasterMSM for the MSM analysis, based on the master equation
You can read the documentation here.
Contributors
This code has been written by David De Sancho and Ion Mitxelena.
Installation
git clone http://github.com/BioKT/AdaptiveMasterMSM destination/AdaptiveMasterMSM
cd destination/AdaptiveMasterMSM
python setup.py install --user
External libraries
mdtraj : https://mdtraj.org
MasterMSM: https://github.com/BioKT/MasterMSM
GROMACS: http://www.gromacs.org