NDSimulator

Documentation: https://ndsimulator.rtfd.io

A molecular dynamics tool for toy model systems.

Features

• model a particle on a N-dimensional energy landscape
• Molecular dynamics, metadynamics, umbrella sampling are implemented.
• Allow users to define collective variables
• Langevin (1st and 2nd order), velocity rescale and NVE ensemble are available for MD

Installation

1. from GitHub

git clone [email protected]:mir-group/NDSimulator.git
pip install -e ./

2. from pip

pip install ndsimulator

Prerequisits

• Python3.8
• matplotlib
• NumPy
• pyfile-utils

Testing

pytest tests

Commandline interface

The inputs specifying the system, method, parameters, and visualization options can be received via an inputs file

ndsimulator examples/2d-md.yaml