Installation

Install dependencies

mstk requires numpy, pandas and rdkit for most of its functionalities. openmm is required for energy calculation, minimization etc… chemfiles is required for parsing XTC and DCD trajectory formats. packmol is required for building simulation box. scipy, scikit-learn and pymbar-core are required by analyzer module.

It is recommended to install these dependencies with conda.

conda install -c conda-forge numpy pandas rdkit openmm chemfiles packmol scipy scikit-learn pymbar-core

Install mstk

mstk itself can be installed either with pip or from source code.

Install mstk with pip

pip install mstk

Install mstk from source code

Clone it from GitHub:

git clone https://github.com/z-gong/mstk

Add the following line to .bashrc so that it can be found by python interpreter:

export PYTHONPATH=$PYTHONPATH:/path/of/mstk
export PATH=$PATH:/path/of/mstk/scripts