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 groponp@gmail.com.
git clone git@github.com:groponp/Jarzynski.git
cd jarzynski
#! create a conda env or python env to manage it.
conda create -n jarzynski python=3.9
conda activate jarzysnki
pip install pyinstaller
pip install -r requirements.txt
#! make executable to PATH
pyinstaller --onefile jarzynski.py
cd dist/
exe=`pwd`
echo "export PATH=\"${exe}:$PATH\"" >> ~/.zshrc #| For macOS
echo "export PATH=\"${exe}:$PATH\"" >> ~/.bashrc #| For linux
source ~/.zshrc #! for macOS
source ~/.bashrc #! for linux
#! test
cd
jarzynski pmf -h
#! return
Usage: jarzynski [options]
<Compute Jarzynski Equality> wrote by: Ropón-Palacios G.
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-f IFILE, --ifile=IFILE
Name of the input file, units inputs: Distance [nm]
and Work [kJ/mol]
-o OFILE, --ofile=OFILE
Name of the output file, units output: PMF [kJ/mol]
-e ENGINE, --engine=ENGINE
Engine that you use to compute [namd, gmx]
-t TEMPERATURE, --temperature=TEMPERATURE
Absolute temperature the MD [K]
-u, --usage Print usage
jarzynski pmf --usage
#! Return
[USAGE ] "%opt1: jarzynski pmf -f work_matrix.csv -o reconstructed_PMF.csv -t 300 -e gmx"
[USAGE ] "%opt2: jarzynski pmf --file=work_matrix.csv --ofile=reconstructed_PMF.csv --temperature=300 --engine=gmx"
jarzynski.py --usage
#! Return
[USAGE ] "%opt1: jarzynski kd -f PMF.csv -o kd.csv -u nM -b 1000 -t 300 -e gmx"
[USAGE ] "%opt2: jarzynski kd --file=PMF.csv --ofile=kd.csv --units=nM --box_volume=1000 --temperature=300 --engine=gmx"