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mdanalysis
mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

692K 2K 830
yesint
pymolar

Repository for molar crate and its dependencies

8K 49 3
rjdkmr
gmx-clusterbyfeatures

Features Based Conformational Clustering of Molecular Dynamics trajectories.

6K 10 3
mdanalysis
mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

5K 2K 830
maicos-devel
maicos

Analyse molecular dynamics simulations of interfacial and confined systems.

4K 12 6
MDAnalysis
mdacli

Command line interface for MDAnalysis

3K 23 8
theochem
qc-iodata

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

3K 162 55
MDAnalysis
membrane-curvature

MDAnalysis tool to calculate membrane curvature.

1K 35 9
patrickfuchs
buildh

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

1K 16 7
kevinshen56714
emc-pypi

Python interface for Enhanced Monte Carlo (EMC)

1K 23 0
RadonPy
radonpy-pypi

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

919 258 47
openpathsampling
openpathsampling

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

812 116 51
bio-phys
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.

783 20 4
JecaTosovic
waternetworkanalysis

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

775 19 2
amepproject
amep

Data analysis package for active and soft matter simulations

540 24 6
StudDavid
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.

507 11 3
Jan8be
metadynminer

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

498 21 5
Becksteinlab
propkatraj

pKa estimates for proteins using an ensemble approach

497 30 6
ss0832
eam-cream-python

CREAM — Compute-shader Rust EAM Atomistics

478 0 0
rjdkmr
dnamd

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

406 30 10
theochem
iodata

Python Input and Output Library for Quantum Chemistry.

402 162 55
BHM-Bob
lazydock

A Python package for molecular docking

381 1 0
ci-lab-cz
streamd

Streamd Python module to facilitate molecular dynamics

376 89 20
t-0hmura
amber-mlips

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

335 1 1
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