molecular-simulation

There are 18 repositories under molecular-simulation topic.

MDAnalysis / mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
molecular-dynamics python science trajectory-analysis molecular-simulation molecular-dynamics-simulation mdanalysis computational-chemistry
Language:Python 1263
nwchemgit / nwchem
NWChem: Open Source High-Performance Computational Chemistry
computational-chemistry parallel-computing electronic-structure-calculations molecular-simulation density-functional-theory nwchem chemistry hartree-fock quantum-chemistry
Language:Fortran 483
torchani
aiqm / torchani
Accurate Neural Network Potential on PyTorch
deep-learning force-field molecular-simulation neural-network quantum-chemistry quantum-mechanics
Language:Python 446
JuliaMolSim / Molly.jl
Molecular simulation in Julia
molecular-dynamics julia protein-structure physics-simulation structural-bioinformatics molecular-simulation lennard-jones
Language:Julia 376
jparkhill / TensorMol
Tensorflow + Molecules = TensorMol
tensorflow molecules neural-network chemistry molecular-dynamics molecular-simulation simulation force-field monte-carlo meta-dynamics machine-learning
Language:Python 271
Acellera / moleculekit
MoleculeKit: Your favorite molecule manipulation kit
molecule machine-learning proteins drug-discovery molecular-modeling molecular-simulation
Language:Python 196
westpa / westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
computational-chemistry molecular-simulation
Language:Python 186
lumol-org / lumol
Universal extensible molecular simulation engine
molecular-dynamics monte-carlo molecular-simulation computational-chemistry atomistic-simulations
Language:Rust 184
mosdef-hub / mbuild
A hierarchical, component based molecule builder
molecular-dynamics python molecular-simulation molecule-builder mbuild mosdef
Language:Python 170
theochem / iodata
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
computational-biology computational-chemistry computational-physics data-parsing file-conversion file-converter file-format-converter file-format-library file-formats input-output json-schema molecular-dynamics molecular-dynamics-simulation molecular-electronic-structure molecular-mechanics molecular-simulation quantum-chemistry quantum-chemistry-packages quantum-chemistry-programs theoretical-chemistry
Language:Python 124
mosdef-hub / foyer
A package for atom-typing as well as applying and disseminating forcefields
molecular-dynamics molecular-simulation force-field python atom-typing foyer disseminating-forcefields
Language:Python 118
aiqm / aimnet
Atoms In Molecules Neural Network Potential
deep-learning chemistry quantum-mechanics quantum-chemistry neural-network molecular-dynamics molecular-simulation molecular-modeling
Language:Python 92
khavernathy / mcmd
Monte Carlo and Molecular Dynamics Simulation Package
molecular-dynamics-simulation polarization monte-carlo pdb molecular-dynamics chemistry physics physics-simulation monte-carlo-simulation periodicity nvt monte-carlo-simulations molecular-simulation molecules atomic gas-dynamics gas-model crystal-structure crystal xyz
Language:C++ 80
biosimspace
OpenBioSim / biosimspace
An interoperable Python framework for biomolecular simulation.
computational-biology computational-chemistry computational-physics drug-discovery interoperability molecular-dynamics reproducibility reproducible-research molecular-simulation biomolecular-simulation free-energy-calculations
Language:Python 68
openforcefield / openff-interchange
A project (and object) for storing, manipulating, and converting molecular mechanics data.
amber forcefield gromacs interoperability lammps molecular-simulation openmm
Language:Python 67
mlund / faunus
A Framework for Metropolis Monte Carlo Simulation of Molecular Systems
monte-carlo-simulation chemistry molecular-simulation physics-simulation metropolis-monte-carlo cpp
Language:C++ 66
lujiarui / Str2Str
Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)
computational-biology conformation-generation diffusion-models generative-models molecular-dynamics molecular-simulation pytorch
Language:Python 59
shirtsgroup / physical_validation
Physical validation of molecular simulations
physical-validation molecular-simulation molecular-dynamics molecular-mechanics python
Language:Python 55
timdecode / LifeBrush
A toolkit for painting agent-based mesoscale molecular simulations and illustrations.
molecular-simulation molecular-biology agent-based-modeling procedural-generation texture-synthesis vr virtual-reality unreal-engine
Language:C++ 49
juexinwang / NRI-MD
Neural relational inference for molecular dynamics simulations
molecular-simulation graph-neural-networks
Language:Python 47
atomify
andeplane / atomify
Real time molecular dynamics in the browser using LAMMPS
atomistic-simulations lammps molecular-dynamics molecular-dynamics-simulation molecular-simulation visualization webassembly webgl
Language:JavaScript 43
MaginnGroup / Cassandra
Cassandra is a Monte Carlo package to conduct atomistic simulations.
monte-carlo-simulation molecular-simulation atomistic-simulations
Language:Fortran 38
sire
OpenBioSim / sire
Sire Molecular Simulations Framework
biomolecular-simulation cplusplus molecular-simulation python free-energy-calculations
Language:C++ 38
lanl / Architector
The architector python package - for 3D metal complex design. C22085
actinides computational-chemistry d-block lanthanides molecular-simulation molecular-structures rare-earth-elements
Language:Python 35
aqlaboratory / pnerf
proteins machine-learning protein-structure molecular-dynamics molecular-simulation molecular-modeling
Language:Python 34
leelasd / OPLSAA-DB
Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.
molecular-dynamics molecular-simulation force-field opls-aa lammps gromacs namd charmm tinker openmm thermodynamics
31
qusers / Q6
Q6 Repository -- EVB, FEP and LIE simulator.
evb molecular-dynamics computational-chemistry molecular-modeling molecular-simulation empirical-valence-bond
Language:Fortran 31
LoLab-MSM / PyBILT
Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.
molecular-dynamics-simulation molecular-simulation analyses molecular-dynamics-trajectories lipids lipid-bilayers
Language:Python 24
Smoren / molecular-ts
Virtual chemistry simultaion. Visualization of the behavior of particles in 2D and 3D space. Artifical life research.
3d canvas molecular-simulation cellular-automaton cheminformatics molecular-dynamics artifical-life
Language:TypeScript 23
Inniag / openmm-scripts-amoeba
:microscope: OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field
molecular-dynamics molecular-simulation polarisation ion-channels amoeba
Language:Python 21
channotation / chap
CHAP is a tool for the functional annotation of ion channel structures:
molecular-dynamics molecular-simulation molecular-dynamics-simulation ion-channel
Language:C++ 18
Matgenix / turbomoleio
Turbomoleio is a python package containing a set of tools for the generation of inputs and parsing of outputs for the TURBOMOLE quantum chemistry package.
computational-chemistry quantum-chemistry molecular-simulation molecular-modeling
Language:Python 18
chimes_calculator
rk-lindsey / chimes_calculator
Tools to interface ChIMES with various external codes.
machine-learning-force-field molecular-simulation computational-chemistry chimes
Language:C++ 18
lmmentel / chemtools
Python tools for quantum chemical calculations
python quantum-chemistry molpro gamessus basis-set optimization molecular-simulation gaussian chemistry computational-chemistry
Language:Python 17
m3g / ComplexMixtures.jl
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
amber chemistry distribution-function gromacs lammps molecular-dynamics molecular-dynamics-simulation molecular-modeling molecular-simulation namd
Language:Julia 14
mlund / coulombgalore
C++ Library for Electrostatics
molecular-simulation cpp14 molecular-dynamics monte-carlo physics chemistry electrostatics multipole dipole intermolecular-interactions
Language:C++ 14