Molecular Dynamics | Ecosyste.ms: Awesome

https://github.com/mdanalysis/pmda

Parallel algorithms for MDAnalysis

analysis dask mdanalysis molecular-dynamics parallel

Last synced: 12 Apr 2025

https://github.com/lilyminium/psiresp

RESP with inter- and intra-molecular constraints in Psi4.

atomic-charges molecular-dynamics psi4 python

Last synced: 14 Apr 2025

https://github.com/deepmodeling/dpti

A Python Package to Automate Thermodynamic Integration Calculations for Free Energy

atomistic-simulations free-energy molecular-dynamics thermodynamic-integration workflow

Last synced: 16 Oct 2025

https://github.com/arm61/pylj

Teaching Utility for Classical Atomistic Simulation.

chemistry computational-chemistry computational-physics education jupyter-notebook molecular-dynamics monte-carlo physics

Last synced: 25 Oct 2025

https://github.com/p-j-smith/lipyphilic

A Python toolkit for the analyis of lipid membrane simulations

lipids molecular-dynamics python3

Last synced: 05 Oct 2025

https://github.com/macrocosm-os/mainframe

Generalized Scientific Compute on BIttensor

bittensor crypto decentralized dft molecular-dynamics

Last synced: 17 Jan 2026

https://github.com/pdebuyl-lab/tidynamics

A tiny package to compute the dynamics of stochastic and molecular simulations

correlation molecular-dynamics numpy stochastic-process

Last synced: 28 Oct 2025

https://github.com/hmcezar/clusttraj

Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.

clustering distance-matrix molecular-dynamics monte-carlo-trajectory openbabel python-script rmsd trajectory

Last synced: 16 Jan 2026

https://github.com/isisneutronmuon/mdanse

MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments

data-analysis molecular-dynamics neutron-scattering python qt-gui science

Last synced: 22 Aug 2025

https://github.com/becksteinlab/mdpow

Calculation of water/solvent partition coefficients with Gromacs.

free-energy gromacs gromacswrapper molecular-dynamics python science

Last synced: 30 Jun 2025

https://github.com/yesint/molar

Repository for molar crate and its dependencies

molecular-dynamics molecular-dynamics-simulation molecular-modeling trajectory-analysis

Last synced: 13 Apr 2025

https://github.com/simongravelle/nmrformd

NMRforMD is a python script for the calculation of NMR relaxation time T1 and T2 from molecular dynamics trajectory file.

fair gromacs lammps molecular-dynamics nmr nmr-spectroscopy open-source python simulations

Last synced: 20 Aug 2025

https://github.com/zincware/ipsuite

Machine Learned Interatomic Potential Tools

machine-learning molecular-dynamics physics zntrack

Last synced: 22 Jul 2025

https://github.com/bio-phys/cnt-gaff

Build atomistic structures of carbon nanotubes with the possibility to add functional groups (OH, COOH, COO-) and assigns generalized Amber (GAFF) parameters to them.

amber carbon-nanotubes force-field gaff molecular-dynamics

Last synced: 16 Jan 2026

https://github.com/pritampanda15/molecular-dynamics

Self explained tutorial for molecular dynamics simulation using gromacs

charmm complex dynamics freeenergy hpc hpc-clusters lipidbilayer molecular molecular-dynamics molecular-dynamics-simulation molecular-mechanics molecular-simulation pca proteinligand simulation

Last synced: 15 Apr 2025

https://github.com/aromanro/eventmoleculardynamics

A program implementing event driven molecular dynamics for hard smooth spheres, using OpenGL for displaying

3d 3d-graphics collision computational-physics event-driven glm lightning mfc molecular-dynamics molecular-dynamics-simulation opengl particles physics physics-simulation shaders simulation sphere

Last synced: 18 Mar 2025

https://github.com/zincware/IPSuite

Machine Learned Interatomic Potential Tools

machine-learning molecular-dynamics physics zntrack

Last synced: 04 May 2025

https://github.com/bio-phys/pydiffusion

Analyse Rotational Diffusion Tensor from MD Simulations

brownian-dynamics diffusion mdanalysis molecular-dynamics python rotation simulation

Last synced: 16 Jan 2026

https://github.com/craabreu/ufedmm

Unified Free Energy Dynamics (UFED) simulations with OpenMM

collective-variables enhanced-sampling free-energy metadynamics molecular-dynamics openmm

Last synced: 07 Oct 2025

https://github.com/matsunagalab/mdtoolbox.jl

MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules

biomolecule differentiable-programming julia molecular-dynamics

Last synced: 15 Apr 2025

https://github.com/lab-cosmo/atomistic-cookbook

A collection of simulation recipes for the atomic-scale modeling of materials and molecules

atomistic-simulations machine-learning modeling molecular-dynamics simulation

Last synced: 03 May 2025

https://github.com/ltalirz/atomistic-software

Tracking citations of atomistic simulation engines

atomistic-simulation-engine atomistic-simulations density-functional-theory electronic-structure force-fields molecular-dynamics quantum-chemistry quantum-monte-carlo tight-binding

Last synced: 13 Apr 2025

https://github.com/mdanalysis/mdacli

Command line interface for MDAnalysis

cli command-line command-line-tool computational-chemistry mdanalysis molecular-dynamics molecular-dynamics-simulation python science trajectory-analysis

Last synced: 23 Jan 2026

https://github.com/rebelot/schrodinger_utils

Various integrations to the Schrodinger ecosystem. With major interest on analysis tools for Molecular Dynamics simulations run with Desmond.

bioinformatics desmond maestro molecular-dynamics mutual-information plumed schrodinger structural-biology

Last synced: 21 Mar 2025

https://github.com/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.

enhanced-sampling molecular-dynamics molecular-dynamics-simulation slurm slurm-cluster

Last synced: 14 Jan 2026

https://github.com/mlund/coulombgalore

C++ Library for Electrostatics

chemistry cpp14 dipole electrostatics intermolecular-interactions molecular-dynamics molecular-simulation monte-carlo multipole physics

Last synced: 28 Feb 2026

https://github.com/chiang-yuan/csh4lmp

The computational modeling tool for custom atomistic model of calcium-silicate-hydrates (C-S-H)

computational-modeling cplusplus lammps-data molecular-dynamics

Last synced: 17 Jun 2025

https://github.com/moldyn/clustering

Robust and stable clustering of molecular dynamics simulation trajectories.

biophysics clustering cpp cuda molecular-dynamics

Last synced: 14 Apr 2025

https://github.com/joaorodrigues/openmm_scripts

Collection of Python scripts to setup and run simulations with OpenMM

biophysics molecular-dynamics openmm python

Last synced: 01 Apr 2026

https://github.com/simongravelle/peggenerator

Generate PEG topology for GROMACS and LAMMPS

gromacs lammps molecular-dynamics peg polyethylene-glycol python3

Last synced: 19 Apr 2025

https://github.com/erwallace/neural-optimiser

Batched optimisation algorithms for neural network potential driven molecular dynamics.

molecular-dynamics molecular-optimization neural-network-potentials torch-geometric

Last synced: 03 Mar 2026

https://github.com/simongravelle/python-for-lammps

Python scripts for dealing with molecular dynamics script for LAMMPS

molecular-dynamics python

Last synced: 19 Apr 2025

https://github.com/weitse-hsu/ensemble_md

A python package for performing GROMACS simulation ensembles

advanced-sampling-methods drug-design expanded-ensembles free-energy-calculations molecular-dynamics parallel-computing protein-simulations python replica-exchange statistical-mechanics

Last synced: 11 Mar 2026

https://github.com/bio-phys/cadishi

Cadishi: CAlculation of DIStance HIstograms

astrophysics capriqorn correlation cuda distance-histogram distribution function gpgpu gpu high-performance histogram molecular-dynamics openmp openmp-parallelization orthorhombic periodic-box python rdf triclinic vectorization

Last synced: 16 Jan 2026

https://github.com/mdanalysis/mdanalysisdata

Access to data for workshops and extended tests of MDAnalysis.

dataset-manager mdanalysis molecular-dynamics python

Last synced: 03 Apr 2026

https://github.com/aspirincode/alphappimd

Exploring the conformational ensembles of protein-protein complexes with transformer-based generative neural networks

ambertools deep-generative-model dockq molecular-dynamics openmm ppi protein-protein-complexes transformers

Last synced: 24 Jul 2025

https://github.com/yuxuanzhuang/ggmolvis

Molecular visualization for MDAnalysis with MolecularNodes in Blender

blender mdanalysis molecular-dynamics molecularnodes visualization

Last synced: 09 Apr 2025

https://github.com/choderalab/chiron

Differentiable Markov Chain Monte Carlo

molecular-dynamics

Last synced: 04 Feb 2026

https://github.com/cbouy/dashmd

Real time monitoring and visualization of Amber MD simulations

ambermd bokeh compchem computational-chemistry molecular-dynamics molecular-modeling ngl

Last synced: 28 Oct 2025

https://github.com/lightonai/newma-md

Conformational exploration SARS-CoV-2 (coronavirus responsible for COVID-19)

change-point-detection covid-19 molecular-dynamics newma photonic-computing

Last synced: 26 Aug 2025

https://github.com/simongravelle/how-to-lammps

How-to perform LAMMPS simulations

advices beginner-friendly how-to inputs lammps molecular-dynamics simulations step-by-step tips-and-tricks

Last synced: 19 Apr 2025

https://github.com/ipudu/order

:potable_water: A tool to characterize the local structure of liquid water by geometric order parameters.

ionic-conductivity molecular-dynamics order-parameters water-structure

Last synced: 14 Jan 2026

https://github.com/initqp/somd

Molecular dynamics package designed for the SIESTA DFT code.

aimd molecular-dynamics neuroevolution-potential siesta

Last synced: 04 May 2025

https://github.com/glotzerlab/freud-examples

Examples for the freud library.

analysis freud glotzer materials-science molecular-dynamics simulation

Last synced: 15 Mar 2026

https://github.com/mphowardlab/lammpsio

Python tools for working with LAMMPS files

lammps molecular-dynamics python

Last synced: 16 Jan 2026

https://github.com/becksteinlab/hop

Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.

mdanalysis molecular-dynamics python science solvation water

Last synced: 28 Feb 2026

https://github.com/jerboaburrow/simplefastopenatomicvisualiser

Visualise atomic and molecular system structures and trajectories

atoms ffmpeg lua molecular-dynamics molecules opengl visualisation

Last synced: 10 Jul 2025

https://github.com/jorisparet/partycls

Unsupervised learning of structure in systems of interacting particles.

clustering machine-learning molecular-dynamics physics python

Last synced: 17 Mar 2026

https://github.com/llnl/user-eph

LAMMPS extension to capture electron-ion interaction. This is a mirror of https://gitlab.com/artuuuro/USER-EPH.

cpp electron-phonon-coupling gpu lammps molecular-dynamics

Last synced: 13 Jun 2025

https://github.com/linux-cpp-lisp/sitator

Unsupervised landmark analysis for jump detection in molecular dynamics simulations.

materials-science molecular-dynamics site-analysis solid-state-physics

Last synced: 01 Aug 2025

https://github.com/rrze-hpc/md-bench

A performance-oriented prototyping harness for state of the art Molecular Dynamics algorithms

benchmark cuda-programming hpc molecular-dynamics scientific-computing

Last synced: 24 Apr 2025

https://github.com/choderalab/integrator-benchmark

Code for enumerating and evaluating numerical methods for Langevin dynamics using near-equilibrium estimates of the KL-divergence. Accompanies https://doi.org/10.3390/e20050318

kl-divergence langevin-dynamics molecular-dynamics openmm

Last synced: 04 Feb 2026

https://github.com/pujanajmera/pycpet

Computing Protein Electric Field Topology in python, built for high-throughput accelerated calculations

computational-chemistry electric-field electrostatics enzyme enzyme-catalysis molecular-dynamics simulation-analysis

Last synced: 31 May 2026

https://github.com/Chenghao-Wu/RobertoMD.jl

Massively parallel hybrid particle-field molecular dynamics (hPF-MD) simulation method in Julia

coarse-grained julia molecular-dynamics particle-field physical-chemistry physical-modeling polymer simulation

Last synced: 27 Mar 2025

https://github.com/pdebuyl/pyh5md

Read and write H5MD files

hdf5 molecular-dynamics

Last synced: 28 Oct 2025

https://github.com/sbischoff-ai/simple-molecular-dynamics

Some C++ code for basic Molecular Dynamics simulations.

molecular-dynamics physics simulation velocity-verlet

Last synced: 23 Oct 2025

https://github.com/conorwilliams/openfly

The open framework for on-the-fly off-lattice kinetic Monte Carlo simulations.

kinetic-monte-carlo molecular-dynamics off-lattice-model on-the-fly particle-simulation simulation

Last synced: 09 Aug 2025

https://github.com/uibcdf/molsysmt

Open source library to work with molecular systems

molecular-dynamics molecular-dynamics-simulation molecular-dynamics-trajectories molecular-modeling molecular-simulation molsysmt python

Last synced: 03 Aug 2025

https://github.com/redesignscience/cvpack

Useful Collective Variables for OpenMM

collective-variables enhanced-sampling metadynamics molecular-dynamics openmm

Last synced: 04 Oct 2025

https://github.com/kevinshen56714/emc-pypi

Python interface for Enhanced Monte Carlo (EMC)

lammps lammps-data lammps-python-interface molecular-dynamics molecular-dynamics-simulation monte-carlo smiles-strings

Last synced: 19 Mar 2025

https://github.com/ejmeitz/simplecrystals.jl

An interface for generating simple crystal structures for molecular dynamics simulations.

atomsbase bravais-lattice crystal julia molecular-dynamics simulation solid-state-physics

Last synced: 13 Jul 2025

https://github.com/chao1224/neuralmd

NeuralMD for protein-ligand binding simulation

binding binding-affinity ligand md molecular-dynamics molecular-dynamics-simulation protein protein-ligand-binding

Last synced: 16 Apr 2025

https://github.com/aimat-lab/nnsformd

Neural network class for molecular dynamics to predict potential energy, forces and non-adiabatic couplings.

ab-initio-simulations excited-states machine-learning molecular-dynamics neural-network potentials

Last synced: 03 Feb 2026

https://github.com/abhishektiwari/hbat

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

bioinformatics bioinformatics-tool chemistry computer-aided-drug-design crystallography drug-discovery halogen-bonds hydrogen-bonds molecular-dynamics molecular-dynamics-simulation molecular-interactions noncovalent-interactions pdb pi-interaction protein-data-bank protein-dna-interactions protein-ligand-interactions protein-protein-interaction structural-bioinformatics structural-biology

Last synced: 13 Jun 2026

https://github.com/seatonullberg/velvet

[WIP] Classical atomistic simulation engine with a focus on user-friendliness and extensibility

atomistic-simulation-engine chemistry computational-chemistry materials-science molecular-dynamics physics simulation

Last synced: 23 Apr 2025

https://github.com/alchemistry/alchemtest

the simple alchemistry test set

datasets free-energy molecular-dynamics science

Last synced: 31 Oct 2025

https://github.com/janjoswig/commonnnclustering

A Python package for common-nearest-neighbours clustering

clustering common-nearest-neighbours density-based-clustering markov-model molecular-dynamics scikit-learn

Last synced: 24 Oct 2025

https://github.com/zincware/znh5md

ZnH5MD - High Performance Interface for H5MD Trajectories

h5md h5py molecular-dynamics science tensorflow-datasets trajectory-analysis

Last synced: 22 Jul 2025

https://github.com/craabreu/openmm-nonbonded-slicing

An OpenMM plugin for slicing nonbonded interactions based on particle classification

alchemical-free-energy enhanced-sampling molecular-dynamics

Last synced: 07 Oct 2025

https://github.com/craabreu/openmm_rigidbody_plugin

Rigid Body Dynamics with OpenMM

molecular-dynamics openmm rigid-bodies

Last synced: 07 Oct 2025

https://github.com/becksteinlab/zarrtraj

zarrtraj MDAKit for @MDAnalysis

file-format mdanalysis molecular-dynamics streaming zarr

Last synced: 23 Apr 2025

https://github.com/choderalab/thresholds

Utilities for determining maximum tolerable timesteps. See https://doi.org/10.3390/e20050318

langevin-dynamics molecular-dynamics nsf-grant-che-1738979 probabilistic-bisection stability-threshold

Last synced: 04 Feb 2026

https://github.com/simongravelle/publication-data

Data and scripts from recent publications

bash data gromacs interface lammps mlpi molecular-dynamics nmr open-data open-research outreach salt scientific-paper soft-matter water

Last synced: 31 Aug 2025

https://github.com/choderalab/yank-benchmark

Standard experimental accuracy benchmark set for YANK.

alchemical-free-energy benchmark benchmark-set free-energy-calculations molecular-dynamics yank

Last synced: 04 Feb 2026

https://github.com/lammpstutorials/lammpstutorials-ebook

LAMMPS tutorials for both beginners and advanced users: the ebook

course ebook lammps molecular-dynamics polymer tutorial

Last synced: 07 Sep 2025

https://github.com/llnl/ezalign

Coarse grain to atomistic molecular coordinate and topology converter

biology molecular-dynamics

Last synced: 29 Apr 2025

https://github.com/timbernat/polymerist

Polymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Tools

molecular-dynamics openforcefield polymerscience

Last synced: 10 Apr 2026

https://github.com/jdrusso/msm_we

History-augmented Markov analysis of weighted ensemble trajectories.

markov-model molecular-dynamics weighted-ensemble

Last synced: 23 Feb 2026

https://github.com/raimis/plumed-pybias

PyBias: PLUMED plug-in with embeded Python

molecular-dynamics python simulations

Last synced: 20 Jun 2025

https://github.com/dnlbauer/xdrfile

Rust Wrapper around the GROMACS libxdrfile library. A low level api to read and write molecular trajectories in .xtc and .trr format.

gromacs molecular-dynamics trajectories trr xdrfile xtc

Last synced: 14 Apr 2025

https://github.com/axsk/isokann.jl

Julia implementation of the ISOKANN algorithm for the computation of invariant subspaces of Koopman operators

isokann molecular-dynamics neural-network package zib

Last synced: 01 Aug 2025

https://github.com/ur-whitelab/peptidesim

Automated peptide simulation tool with gromacs, gromacswrapper, plumed

gromacs molecular-dynamics peptides

Last synced: 14 Jul 2025

https://github.com/allisterb/onemd

Data-parallel molecular dynamics simulator for Intel oneAPI.

cpp cpp17 devcloud dpcpp intel molecular-dynamics simulation

Last synced: 12 Mar 2026

https://github.com/lammpstutorials/old-lammps-inputs

LAMMPS tutorials for both beginners and advanced users

beginner lammps lammps-data lammps-input molecular-dynamics molecular-dynamics-simulation step-by-step tutorial

Last synced: 07 Sep 2025

https://github.com/craabreu/mics

A friendly Python library for multistate analysis with MICS and MBAR

free-energy mixture-model molecular-dynamics monte-carlo multistate-bennett-acceptance-ratio statistics

Last synced: 07 Oct 2025

https://github.com/chiang-yuan/muse

A python package for fast building amorphous solids and liquid mixtures from @materialsproject computed structures and machine learning interatomic potentials

atomistic-simulations high-throughput interatomic-potentials machine-learning materials molecular-dynamics

Last synced: 19 Apr 2026

https://github.com/bartbruininks/mdvcontainment

Robust characterization of inside and outside in periodic spaces.

containment graph md molecular-dynamics point-cloud segmentation topology visualization voxels

Last synced: 22 Apr 2025

https://github.com/edwardsmith999/flowmol

A molecular dynamics solver for molecular fluid dynamics simulation

fluid-dynamics molecular-dynamics parallel simulation

Last synced: 06 Mar 2026

https://github.com/glasagent/amorphouspy

Workflows for computing glass properties at the atomic level

amorphous-materials atomistic-simulations force-fields glass molecular-dynamics

Last synced: 30 May 2026

https://github.com/ml-jku/lam-slide

Code for the paper LaM-SLidE - Latent Space Modeling of Spatial Dynamical Systems via Linked Entities

dynamical-systems flow-matching latent-diffusion latent-space molecular-dynamics molecular-dynamics-simulation simulation

Last synced: 08 May 2025

https://github.com/uibcdf/academia

Este repositorio debe ser el punto de partida y encuentro para cualquier investigador o estudiante que quiera comenzar a trabajar con/en la UIBCDF. Si has caído aquí por otro motivo y este material te es útil, eres más que bienvenido a usarlo e interaccionar con nosotros.

academic-project cc-by-sa conda drug-design drug-discovery git github jupyter molecular-dynamics molecular-dynamics-simulation python spanish-language tutorials