jarzynski 1.0.4

A computational tool to compute PMF and Kd from non-equilibrium simulation

Jarzynski Tool

This repository contains a python script, which allows to rebuild the PMF based on the Jarzysnki Equality framework. For this you need to pass a file in CSV format, where you have the work values ​​(kcal/mol/A) of all the replicas, the first column has to be the distance in (Angstrom). If you have any questions, you can contact me at [e-mail].

Usage Jarzynski

python jarzynski.py pmf --usage 

#! Return 
[USAGE    ] "%opt1: python jarzynski.py pmf -f work_matrix.csv -o reconstructed_PMF.csv -t 300 -e gmx"
[USAGE    ] "%opt2: python jarzynski.py pmf --file=work_matrix.csv --ofile=reconstructed_PMF.csv --temperature=300 --engine=gmx"

Usage Kd

python jarzynski.py kd --usage 

#! Return 
[USAGE    ] "%opt1: python jarzynski.py kd -f PMF.csv -o kd.csv -u nM -b 1000 -t 300 -e gmx"
[USAGE    ] "%opt2: python jarzynski.py kd --file=PMF.csv --ofile=kd.csv --units=nM --box_volume=1000 --temperature=300 --engine=gmx"

License

GPLv3