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 1484
nwchemgit / nwchem
NWChem: Open Source High-Performance Computational Chemistry
chemistry computational-chemistry density-functional-theory electronic-structure-calculations hartree-fock molecular-simulation nwchem parallel-computing quantum-chemistry
Language:Fortran 574
torchani
aiqm / torchani
TorchANI 2.0 is an open-source library that supports training, development, and research of ANI-style neural network interatomic potentials. It was originally developed and is currently maintained by the Roitberg group.
deep-learning force-field molecular-simulation neural-network pytorch quantum-chemistry quantum-mechanics
Language:Python 526
JuliaMolSim / Molly.jl
Molecular simulation in Julia
julia lennard-jones molecular-dynamics molecular-simulation physics-simulation protein-structure structural-bioinformatics
Language:Julia 447
jparkhill / TensorMol
Tensorflow + Molecules = TensorMol
chemistry force-field machine-learning meta-dynamics molecular-dynamics molecular-simulation molecules monte-carlo neural-network simulation tensorflow
Language:Python 275
Acellera / moleculekit
MoleculeKit: Your favorite molecule manipulation kit
molecule machine-learning proteins drug-discovery molecular-modeling molecular-simulation
Language:Python 226
westpa / westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
computational-chemistry molecular-simulation
Language:Python 207
lumol-org / lumol
Universal extensible molecular simulation engine
molecular-dynamics monte-carlo molecular-simulation computational-chemistry atomistic-simulations
Language:Rust 205
mosdef-hub / mbuild
A hierarchical, component based molecule builder
molecular-dynamics python molecular-simulation molecule-builder mbuild mosdef
Language:Python 200
theochem / iodata
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
quantum-chemistry quantum-chemistry-programs quantum-chemistry-packages computational-chemistry computational-biology computational-physics file-format-converter data-parsing json-schema theoretical-chemistry molecular-mechanics molecular-dynamics molecular-simulation input-output file-formats file-format-library molecular-dynamics-simulation file-conversion file-converter molecular-electronic-structure
Language:Python 137
mosdef-hub / foyer
A package for atom-typing as well as applying and disseminating forcefields
atom-typing disseminating-forcefields force-field foyer molecular-dynamics molecular-simulation python
Language:Python 134
biosimspace
OpenBioSim / biosimspace
An interoperable Python framework for biomolecular simulation.
biomolecular-simulation computational-biology computational-chemistry computational-physics drug-discovery free-energy-calculations interoperability molecular-dynamics molecular-simulation reproducibility reproducible-research
Language:Python 126
aiqm / aimnet
Atoms In Molecules Neural Network Potential
chemistry deep-learning molecular-dynamics molecular-modeling molecular-simulation neural-network quantum-chemistry quantum-mechanics
Language:Python 106
khavernathy / mcmd
Monte Carlo and Molecular Dynamics Simulation Package
atomic chemistry crystal crystal-structure gas-dynamics gas-model molecular-dynamics molecular-dynamics-simulation molecular-simulation molecules monte-carlo monte-carlo-simulation monte-carlo-simulations nvt pdb periodicity physics physics-simulation polarization xyz
Language:C++ 92
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 80
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 78
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++ 72
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 67
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:C++ 64
juexinwang / NRI-MD
Neural relational inference for molecular dynamics simulations
molecular-simulation graph-neural-networks
Language:Python 59
sire
OpenBioSim / sire
Sire Molecular Simulations Framework
biomolecular-simulation cplusplus molecular-simulation python free-energy-calculations qmmm
Language:C++ 59
DrugBud-Suite / CADD_Vault
chemistry cheminformatics chemoinformatics computational-chemistry computational-biology computational-physics compchem drug-discovery drugs drug-repurposing drug-design protein-ligand-interactions virtual-screening molecular-dynamics molecular-modeling molecular-simulation sbvs
Language:HTML 57
shirtsgroup / physical_validation
Physical validation of molecular simulations
molecular-dynamics molecular-mechanics molecular-simulation physical-validation python
Language:Python 57
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++ 55
MaginnGroup / Cassandra
Cassandra is a Monte Carlo package to conduct atomistic simulations.
monte-carlo-simulation molecular-simulation atomistic-simulations
Language:Fortran 46
Smoren / molecular-ts
Virtual chemistry simultaion. Particle automata. 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 particle-automata
Language:TypeScript 43
pritampanda15 / Molecular-Dynamics
Self explained tutorial for molecular dynamics simulation using gromacs
charmm complex dynamics freeenergy hpc hpc-clusters molecular pca simulation lipidbilayer proteinligand molecular-dynamics molecular-dynamics-simulation molecular-mechanics molecular-simulation
Language:Shell 37
aqlaboratory / pnerf
proteins machine-learning protein-structure molecular-dynamics molecular-simulation molecular-modeling
Language:Python 36
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
35
qusers / Q6
Q6 Repository -- EVB, FEP and LIE simulator.
evb molecular-dynamics computational-chemistry molecular-modeling molecular-simulation empirical-valence-bond
Language:Fortran 34
LoLab-MSM / PyBILT
Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.
analyses lipid-bilayers lipids molecular-dynamics-simulation molecular-dynamics-trajectories molecular-simulation
Language:Python 26
Inniag / openmm-scripts-amoeba
:microscope: OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field
amoeba ion-channels molecular-dynamics molecular-simulation polarisation
Language:Python 25
chimes_calculator
rk-lindsey / chimes_calculator
Tools to interface ChIMES with various external codes.
chimes computational-chemistry machine-learning-force-field molecular-simulation
Language:C++ 22
channotation / chap
CHAP is a tool for the functional annotation of ion channel structures:
ion-channel molecular-dynamics molecular-dynamics-simulation molecular-simulation
Language:C++ 21
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 21
lmmentel / chemtools
Python tools for quantum chemical calculations
basis-set chemistry computational-chemistry gamessus gaussian molecular-simulation molpro optimization python quantum-chemistry
Language:Python 20