molecular-dynamics-simulation

There are 28 repositories under molecular-dynamics-simulation topic.

brucefan1983 / CUDA-Programming
Sample codes for my CUDA programming book
cuda-programming gpu-programming molecular-dynamics-simulation
Language:Cuda 1924
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
brucefan1983 / GPUMD
Graphics Processing Units Molecular Dynamics
molecular-dynamics-simulation heat-transport cuda molecular-dynamics gpumd phonon gpu machine-learning physics-simulation simulation neural-network neuroevolution natural-evolution-strategies high-performance-computing machine-learning-potential
Language:Cuda 662
Allen-Tildesley / examples
Fortran and Python examples to accompany the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Code" button, or follow the "Releases" link below.
molecular-dynamics molecular-dynamics-simulation monte-carlo monte-carlo-simulation
Language:Fortran 330
brucefan1983 / Molecular-Dynamics-Simulation
Sample codes for my book on molecular dynamics simulation
molecular-dynamics molecular-dynamics-simulation
Language:Jupyter Notebook 262
RadonPy / RadonPy
RadonPy is a Python library to automate physical property calculations for polymer informatics.
modeling polymer simulation molecular-dynamics molecular-dynamics-simulation data-driven-design data-science high-throughput-computing lammps materials-informatics materials-science polymer-simulation psi4 rdkit polymer-informatics
Language:Python 218
choderalab / yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
molecular-dynamics molecular-dynamics-simulation alchemical-free-energy-calculations drug-discovery free-energy openmm mskcc python alchemical free-energy-perturbation
Language:Python 188
MobleyLab / drug-computing
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
drug-discovery python molecular-dynamics molecular-dynamics-simulation monte-carlo docking ligand-screening solubility teaching-materials educational-software
Language:Jupyter Notebook 159
SciML / NBodySimulator.jl
A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics
molecular-dynamics molecular-dynamics-simulation sciml scientific-machine-learning automatic-differentiation algorithmic-differentiation differentiable-programming symbolic-integration geometric-algorithms
Language:Julia 137
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
SENPAI
Chelsea486MHz / SENPAI
Molecular dynamics simulation software
molecular-dynamics chemistry molecular-dynamics-simulation simulation science science-research research cheminformatics
Language:C 133
lammpstutorials / lammpstutorials.github.io
LAMMPS tutorials for both beginners and advanced users
lammps molecular-dynamics molecular-dynamics-simulation monte-carlo-simulation lammps-tutorials lammps-script course step-by-step tutorial beginner carbon cnt electrolyte graphene nanotube pmf polymer charge reaxff simulation
Language:Shell 125
openpathsampling / openpathsampling
An open source Python framework for transition interface and path sampling calculations.
biomolecular-simulation molecular-dynamics molecular-dynamics-simulation molecular-modeling path-sampling monte-carlo
Language:Python 114
m3g / CellListMap.jl
Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc.
minimum-distances molecular-dynamics molecular-dynamics-simulation
Language:Julia 98
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
ci-lab-cz / streamd
Fully automated high-throughput MD pipeline
gromacs gromacs-tools molecular-dynamics molecular-dynamics-simulation
Language:Python 84
Isra3l / ligpargen
molecular-dynamics molecular-dynamics-simulation opls opls-aa cm1a alchemical-free-energy-calculations monte-carlo-simulation
Language:Python 75
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
aromanro / SolarSystem
A solar system simulator with Verlet, using OpenGL for displaying.
physics computational-physics physics-simulation solarsystem planet moon solar opengl glm lightning shadow xml gravitation shaders molecular-dynamics molecular-dynamics-simulation mfc simulation 3d-graphics 3d
Language:C++ 61
wolberlab / pyrod
PyRod - Tracing water molecules in molecular dynamics simulations
molecular-dynamics-simulation pharmacophore water python3
Language:Python 54
choderalab / ensembler
Automated omics-scale protein modeling and simulation setup.
python molecular-dynamics-simulation homology-modeling modeller superfamily
Language:Python 53
Mantevo / miniMD
MiniMD Molecular Dynamics Mini-App
snl-mini-apps molecular-dynamics molecular-dynamics-simulation mini-app mantevo
Language:C++ 50
dadaoqiuzhi / RMD_Digging
RMD_digging is aimed to provide pre-processing and post-processing tools for the reactive molecular dynamics (ReaxFF) simulations based on MATLAB language, including formatting the reactive force field parameters, statistic anasysis of structures, trajectories and mechanisms and output of the visualization files.
lammps materials-studio matlab molecular-dynamics-simulation reaction-mechanism reactive-molecular-dynamics reaxff statistic-analysis visulization vmd
Language:MATLAB 48
protocaller / ProtoCaller
Full automation of relative protein-ligand binding free energy calculations in GROMACS
free-energies gromacs ligand-binding molecular-dynamics-simulation python high-throughput
Language:Python 45
seams-core
d-SEAMS / seams-core
The d-SEAMS C++ core engine
molecular-dynamics-simulation molecular-dynamics trajectory-analysis lua nix d-seams analysis-framework trajectories
Language:C++ 40
smparker / molecular-blender
blend molecules!
python blender molecular-dynamics-simulation molecular-modeling molecular-visualization quantum-chemistry
Language:Python 40
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
yesint / molar
Repository for molar crate and its dependencies
molecular-dynamics molecular-dynamics-simulation molecular-modeling trajectory-analysis
Language:Rust 37
LABIOQUIM / visualdynamics
Web Platform made with Python and NextJS for automating GROMACS simulations
grace gromacs md molecular-dynamics molecular-dynamics-simulation molecular-dynamics-automation
Language:TypeScript 36
Mjolnir-MD / Mjolnir
:zap: general purpose coarse-grained molecular dynamics simulation package
molecular-dynamics-simulation c-plus-plus-11 coarse-grained c-plus-plus science simulation openmp
Language:C++ 35
MDAnalysis / membrane-curvature
MDAnalysis tool to calculate membrane curvature.
mdanalysis molecular-dynamics-simulation python trajectory-analysis
Language:Python 34
Allen-Tildesley / corrections
Corrections to the text of the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017)
molecular-dynamics molecular-dynamics-simulation monte-carlo monte-carlo-simulation
32
ls1mardyn / ls1-mardyn
ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.
molecular-dynamics molecular-dynamics-simulation simulation scientific-computing ls1-mardyn nanofluidics autopas
Language:C++ 32
MolSSI / covid
MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store
covid-19 covid19-data sars-cov-2 molecular-dynamics molecular-dynamics-simulation md-simulations
Language:HTML 31
datreant / MDSynthesis
a logistics and persistence engine for the analysis of molecular dynamics trajectories
molecular-dynamics-simulation mdanalysis python science database
Language:Python 30
Becksteinlab / propkatraj
pKa estimates for proteins using an ensemble approach
molecular-dynamics-simulation pka-predictions mdanalysis pandas
Language:Python 29