Step-by-Step Molecular Simulations with Python
The goal of Step-by-S Molecular Simulations with Python (MoleSimPy) is to write a simple code containing most of the basic functionalities of molecular simulations, including:
- Energy minimization,
- Molecular dynamics,
- Monte Carlo move.
The Python code that is written here is used to realize molecular scientific projects. Note that the code is slow and that efficiency is not the primary objective here.
Contributing
We welcome contributions from the community. Before you start, please read our Contributing Guidelines. These guidelines will help you understand the process and expectations for contributing to the project.
Prerequisite
The target audience includes people who are either completely new to molecular simulations or users of open-source codes such as LAMMPS and GROMACS who want to better understand what is behind those codes. Although some basic knowledge of coding, thermodynamics, and statistical physics is recommended for a full understanding of molecular simulations, MoleSimPy can be followed even without deep expertise in these fields.
What is not (yet) in the code
- molecules/shake,
- electrostatic
- Monte Carlo
- thermostats and barostats other than Berendsen,
- energy minimization methods other than the steepest descent.
Authors
Project creator
- Simon Gravelle: computer physicist in soft matter and fluids at interfaces.
Contributors
Acknowledgments and license
This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101065060. All inputs, scripts, and data files are released under the GNU General Public License v3.0. The released files have been uploaded to Zenodo, under its DOI.