NDSimulator
NDSimulator is an open-source package for running (accelerated) molecular dynamics at N-dimensional space
Contents:
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
from GitHub
git clone git@github.com:mir-group/NDSimulator.git
pip install -e ./
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
