Molecular Dynamics Simulation Python Packages

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

pymolar

Repository for molar crate and its dependencies

mdacli

Command line interface for MDAnalysis

gmx-clusterbyfeatures

Features Based Conformational Clustering of MD trajectories. See details at:

maicos

Analyse molecular dynamics simulations of interfacial and confined systems.

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.

buildh

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

waternetworkanalysis

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

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.

emc-pypi

Python interface for Enhanced Monte Carlo (EMC)

lazydock

LazyDock: Lazy Dock, Easy Life

amep

Python data analysis package for active and soft matter simulations

biofilmsimulation

This repository contains the code for simulating the growth of a Biofilm after attachment using Molecular dynamics simulation methods. The project was build as part of the iGEM 2020 Contest. The BiofilmSimulation software can be installed as A python package, documented under https://pypi.org/project/BiofilmSimulation.

asyncmd

asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax.

iodata

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

propkatraj

pKa estimates for proteins using an ensemble approach

rcbs-py

RCBS.py (Reactivity of Chemical and Biochemical Systems) is a Python package that contains several scripts, functions and classes that simplify the analysis of chemical and biochemical simulations.

metadynminer

Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.

dnamd

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

amber-mlips

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