Molecular Dynamics Simulation Python Packages

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

pymolar

Repository for molar crate and its dependencies

gmx-clusterbyfeatures

Features Based Conformational Clustering of Molecular Dynamics trajectories.

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

maicos

Analyse molecular dynamics simulations of interfacial and confined systems.

mdacli

Command line interface for MDAnalysis

qc-iodata

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

membrane-curvature

MDAnalysis tool to calculate membrane curvature.

emc-pypi

Python interface for Enhanced Monte Carlo (EMC)

buildh

:computer: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.

radonpy-pypi

RadonPy is a Python library to automate physical property calculations for polymer informatics.

openpathsampling

An open source Python framework for transition interface and path sampling calculations.

asyncmd

asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax. Computationally costly operations can be performed locally or submitted to a queuing system.

waternetworkanalysis

Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis

amep

Data analysis package for active and soft matter simulations

propkatraj

pKa estimates for proteins using an ensemble approach

metadynminer

Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations.

eam-cream-python

CREAM — Compute-shader Rust EAM Atomistics

biofilmsimulation

The model applies methods from molecular dynamics (MD) and takes into account different physical and biological effects. The software provides great flexibility by enabling the user to switch easily between sets of constants e.g. to model different bacterial strains. Furthermore, the software includes functions for visualisation of the models behaviour over time.

iodata

Python Input and Output Library for Quantum Chemistry.

dnamd

To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories

lazydock

A Python package for molecular docking

streamd

Streamd Python module to facilitate molecular dynamics

amber-mlips

MLIP wrapper for AMBER QM/MM (UMA, ORB, MACE, AIMNet2)