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Molecular Dynamics

Molecular dynamics allows the atoms and molecules to interact for a fixed period of time, giving a view of the dynamic “evolution” of the system.

https://github.com/lammps/lammps

Public development project of the LAMMPS MD software package

kokkos lammps molecular-dynamics simulation

Last synced: 29 Oct 2024

https://github.com/openmm/openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

molecular-dynamics simulation

Last synced: 07 Nov 2024

https://github.com/deepmodeling/deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

ase c computational-chemistry cpp cuda deep-learning deepmd ipi lammps materials-science molecular-dynamics nodejs potential-energy python pytorch rocm tensorflow

Last synced: 15 Oct 2024

https://github.com/chemlab/chemlab

The chemistry library you were waiting for

chemistry molecular-dynamics molecular-graphics physics python

Last synced: 07 Aug 2024

https://github.com/Colvars/colvars

Collective variables library for molecular simulation and analysis programs

collective-variables enhanced-sampling free-energy gromacs lammps molecular-dynamics namd simulation tinkerhp vmd

Last synced: 03 Aug 2024

https://github.com/becksteinlab/gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

gromacs gromacswrapper molecular-dynamics python science

Last synced: 10 Nov 2024

https://github.com/autodesk/molecular-design-toolkit

Notebook-integrated tools for molecular simulation and visualization

chemistry docker jupyter molecular-dynamics notebook python quantum-chemistry simulation

Last synced: 08 Nov 2024

https://github.com/stefanch/sGDML

sGDML - Reference implementation of the Symmetric Gradient Domain Machine Learning model

gaussian-process machine-learning molecular-dynamics molecular-force-fields quantum-chemistry

Last synced: 13 Nov 2024

https://github.com/abelcarreras/dynaphopy

Phonon anharmonicity analysis from molecular dynamics

anharmonicity lammps molecular-dynamics phonon phonopy vasp

Last synced: 14 Nov 2024

https://github.com/marrink-lab/vermouth-martinize

Describe and apply transformation on molecular structures and topologies

hacktoberfest molecular-dynamics

Last synced: 10 Nov 2024

https://github.com/openmm/NNPOps

High-performance operations for neural network potentials

cuda gpu machine-learning molecular-dynamics molecular-modeling

Last synced: 13 Nov 2024

https://github.com/thorben-frank/mlff

Build neural networks for machine learning force fields with JAX

deep-learning force-fields machine-learning molecular-dynamics

Last synced: 13 Nov 2024

https://github.com/uf3/uf3

UF3: a python library for generating ultra-fast interatomic potentials

force-fields interatomic-potentials machine-learning materials-science molecular-dynamics

Last synced: 13 Nov 2024

https://github.com/carlocamilloni/structural-bioinformatics

This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202

molecular-dynamics structural-bioinformatics structural-biology teaching-materials

Last synced: 02 Nov 2024

https://github.com/NQCD/NQCDynamics.jl

Fast and flexible nonadiabatic molecular dynamics in Julia!

molecular-dynamics monte-carlo nonadiabatic physics-simulation quantum-classical semi-classical

Last synced: 30 Oct 2024

https://github.com/llnl/qball

Qball (also known as qb@ll) is a first-principles molecular dynamics code that is used to compute the electronic structure of atoms, molecules, solids, and liquids within the Density Functional Theory (DFT) formalism. It is a fork of the Qbox code by Francois Gygi.

c-plus-plus cpp dft molecular-dynamics mpi qbox simulation tddft

Last synced: 11 Nov 2024

https://github.com/whitead/symd

N-Dimensional MD engine with symmetry group constraints written in C

c crystallography molecular-dynamics python symmetry

Last synced: 14 Nov 2024

https://github.com/markovmodel/molpx

IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook

free-energy ipython-notebook jupyter-notebook molecular-dynamics tica visualization widget

Last synced: 11 Oct 2024

https://github.com/insilichem/ommprotocol

A command line application to launch molecular dynamics simulations with OpenMM

amber command-line molecular-dynamics openmm

Last synced: 10 Nov 2024

https://github.com/llnl/mgmol

MGmol is a scalable O(N) First-Principles Molecular Dynamics code that is capable of performing large-scale electronics structure calculations and molecular dynamics simulations of atomistic systems.

cpp molecular-dynamics simulation

Last synced: 11 Nov 2024

https://github.com/tongzhugroup/mddatasetbuilder

A script to build reference datasets for training neural network potentials from given LAMMPS trajectories.

chemistry dataset md molecular-dynamics neural-network python

Last synced: 12 Oct 2024

https://github.com/mir-group/pair_allegro

LAMMPS pair style for Allegro deep learning interatomic potentials with parallelization support

gpu kokkos lammps machine-learning molecular-dynamics pytorch

Last synced: 13 Nov 2024

https://github.com/mdanalysis/pmda

Parallel algorithms for MDAnalysis

analysis dask mdanalysis molecular-dynamics parallel

Last synced: 14 Nov 2024

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

A Python toolkit for the analyis of lipid membrane simulations

lipids molecular-dynamics python3

Last synced: 14 Nov 2024

https://github.com/lilyminium/psiresp

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

atomic-charges molecular-dynamics psi4 python

Last synced: 15 Oct 2024

https://github.com/labioquim/visualdynamics

Web Platform made with Python and NextJS for automating GROMACS simulations

grace gromacs md molecular-dynamics molecular-dynamics-automation molecular-dynamics-simulation

Last synced: 12 Oct 2024

https://github.com/becksteinlab/mdpow

Calculation of water/solvent partition coefficients with Gromacs.

free-energy gromacs gromacswrapper molecular-dynamics python science

Last synced: 10 Nov 2024

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: 11 Oct 2024

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: 29 Oct 2024

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: 16 Oct 2024

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: 08 Nov 2024

https://github.com/zincware/IPSuite

Machine Learned Interatomic Potential Tools

machine-learning molecular-dynamics physics zntrack

Last synced: 13 Nov 2024

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: 28 Oct 2024

https://github.com/apax-hub/apax

A flexible and performant framework for training machine learning potentials.

computational-chemistry force-fields interatomic-potentials jax machine-learning materials-science molecular-dynamics quantum-chemistry

Last synced: 13 Nov 2024

https://github.com/simongravelle/peggenerator

Generate PEG topology for GROMACS and LAMMPS

gromacs lammps molecular-dynamics peg polyethylene-glycol python3

Last synced: 08 Nov 2024

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: 11 Oct 2024

https://github.com/mdanalysis/mdanalysisdata

Access to data for workshops and extended tests of MDAnalysis.

dataset-manager mdanalysis molecular-dynamics python

Last synced: 06 Nov 2024

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: 11 Nov 2024

https://github.com/initqp/somd

Molecular dynamics package designed for the SIESTA DFT code.

aimd molecular-dynamics neuroevolution-potential siesta

Last synced: 13 Nov 2024

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: 28 Oct 2024

https://github.com/pdebuyl/pyh5md

Read and write H5MD files

hdf5 molecular-dynamics

Last synced: 11 Oct 2024

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: 30 Oct 2024

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: 10 Nov 2024

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

Python scripts for dealing with molecular dynamics script for LAMMPS

molecular-dynamics python

Last synced: 08 Nov 2024

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: 08 Nov 2024

https://github.com/joaorodrigues/openmm_scripts

Collection of Python scripts to setup and run simulations with OpenMM

biophysics molecular-dynamics openmm python

Last synced: 13 Oct 2024

https://github.com/llnl/ezalign

Coarse grain to atomistic molecular coordinate and topology converter

biology molecular-dynamics

Last synced: 11 Nov 2024

https://github.com/jdrusso/msm_we

History-augmented Markov analysis of weighted ensemble trajectories.

markov-model molecular-dynamics weighted-ensemble

Last synced: 13 Nov 2024

https://github.com/becksteinlab/zarrtraj

zarrtraj MDAKit for @MDAnalysis

file-format mdanalysis molecular-dynamics streaming zarr

Last synced: 10 Nov 2024

https://github.com/li012589/xyzFile2Animation

A small python script to create animation from multiply xyz files

animation molecular-dynamics xyz xyz-files

Last synced: 05 Aug 2024

https://github.com/allisterb/onemd

Data-parallel molecular dynamics simulator for Intel oneAPI.

cpp cpp17 devcloud dpcpp intel molecular-dynamics simulation

Last synced: 07 Nov 2024

https://github.com/sizmailov/pyxmolpp2

Processing and analysis of MD trajectories

analysis cxx md molecular-dynamics pdb python

Last synced: 09 Nov 2024

https://github.com/jbarnoud/simoji

Run a GROMACS simulation with emojis!

emoji gromacs molecular-dynamics

Last synced: 06 Nov 2024

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: 10 Nov 2024

https://github.com/janjoswig/mdparser

Parsers for Molecular Dynamics related file types

gromacs molecular-dynamics parsing python topology

Last synced: 28 Oct 2024

https://github.com/vtlim/plot_potential

Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.

computational-chemistry cosine coulomb-interactions energy-functions forcefield harmonic lennard-jones matplotlib molecular-dynamics molecular-modeling molecular-simulation morse potential presentation-materials vdw

Last synced: 15 Oct 2024

https://github.com/ricalessandri/martini3-mappings

Mapping small-molecules to Martini 3 coarse-grained representations

coarse-graining martini3 molecular-dynamics

Last synced: 12 Oct 2024

https://github.com/njzjz/kconmd

Molecular dynamics (MD) simulations supported by k-Bags Convolutional Neural Network (kcon).

chemistry convolutional-neural-network deep-learning molecular-dynamics python3 tensorflow

Last synced: 28 Oct 2024

https://github.com/somajitdey/progrep

progrep is a command-line tool (Linux) to show live progress report, status and stats of a running simulation or compute job that executes a given number of iterations. It shows % completed, time remaining(ETA), time elapsed (both wall-clock & CPU time), number of threads, MPI_Rank(if any), CPU usage & speed (FPS). The FPS measures may be used in benchmarking, for example, while optimizing HPC algorithms for performance. progrep supports both serial (single-core/single-threaded) and parallel (multicore and/or multinode - e.g. OpenMP and/or MPI) jobs. progrep can also report for jobs running on remote hosts [Case in point: jobs running on Linux Clusters]. progrep works in client-server model. The server for progrep can be installed in your simulation source code with only 4 extra lines (API). When the progrep command is invoked, it queries this server as a client. progrep does not interfere with or slow down your simulation when not invoked. Even when invoked, the overhead is insignificant. Out of the box, the progrep API works with code written in Fortran, C and C++. If your code uses other language, please write your own wrapper for the API. The API library is small and static which benefits portability of your progrep-aware binary.

molecular-dynamics simulations

Last synced: 26 Oct 2024

https://github.com/petercollingridge/atomic.js

A Javascript library for building simple atomic simulations.

canvas chemistry javascript molecular-dynamics simulation

Last synced: 12 Oct 2024

https://github.com/dnlbauer/xdrfile

Rust Wrapper around the GROMACS libxdrfile library. A low level api to read and write .xtc and .trr files.

gromacs molecular-dynamics trajectories trr xdrfile xtc

Last synced: 15 Oct 2024

https://github.com/lukaswittmann/molecular-dynamics-sim

Molecular dynamics simulator I programmed in order to understand MD in more detail. Periodic boundary conditions, energy minimizer, thermostat and barostat, aswell as a correct physical scale and forcefields for the noble gasses are already implemented and working well. Future steps will include parallelization of the calculation of particle interactions and maybe introducing electrostatics and complex molecules like water.

chemistry molecular-dynamics molecular-dynamics-simulation simulation

Last synced: 06 Nov 2024

https://github.com/ricalessandri/evaporate

Generate soft matter blends via simulated solvent evaporation

evaporation molecular-dynamics soft-matter-blends

Last synced: 12 Oct 2024

https://github.com/abelcarreras/gromorg

A python GROMACS interface for MD simulations of organic molecular crystals

gromacs molecular-dynamics molecular-mechanics python simulation

Last synced: 07 Nov 2024

https://github.com/arm61/falass

Neutron and X-ray Reflectometry from Computer Simulation

molecular-dynamics molecular-dynamics-simulation neutron reflectivity reflectometry simulation x-ray

Last synced: 13 Nov 2024

https://github.com/insilichem/tangram_mmsetup

A graphical interface to run OpenMM simulations in UCSF Chimera.

molecular-dynamics openmm ucsf-chimera

Last synced: 10 Nov 2024

https://github.com/joaorodrigues/pbc_mindist

Python code to calculate distances between periodic images in molecular dynamics simulations.

bioinformatics cython molecular-dynamics protein-structure python3 simulations

Last synced: 13 Oct 2024

Molecular Dynamics Awesome Lists
awesome-python-chemistry 149 best-of-atomistic-machine-learning 296
Molecular Dynamics Categories
Interatomic Potentials (ML-IAP) 63 Representation Learning 42 General Tools 28 Language Models 24 Simulations 22 General Chemistry 19 Community resources 17 Representation Engineering 16 Datasets 15 Molecular Dynamics 14 Generative Models 13 Density functional theory (ML-DFT) 11 Universal Potentials 11 Mathematical tools 10 Visualization 10 Educational Resources 9 Molecular Visualization 8 Data Structures 7 Materials Discovery 7 Wavefunction methods (ML-WFT) 5