molecular-dynamics-simulation
There are 392 repositories under molecular-dynamics-simulation topic.
brucefan1983/CUDA-Programming
Sample codes for my CUDA programming book
MDAnalysis/mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
brucefan1983/GPUMD
Graphics Processing Units Molecular Dynamics
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.
brucefan1983/Molecular-Dynamics-Simulation
Sample codes for my book on molecular dynamics simulation
RadonPy/RadonPy
RadonPy is a Python library to automate physical property calculations for polymer informatics.
choderalab/yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
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.
SciML/NBodySimulator.jl
A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics
theochem/iodata
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
Chelsea486MHz/SENPAI
Molecular dynamics simulation software
lammpstutorials/lammpstutorials.github.io
LAMMPS tutorials for both beginners and advanced users
openpathsampling/openpathsampling
An open source Python framework for transition interface and path sampling calculations.
m3g/CellListMap.jl
Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc.
khavernathy/mcmd
Monte Carlo and Molecular Dynamics Simulation Package
ci-lab-cz/streamd
Fully automated high-throughput MD pipeline
andeplane/atomify
Real time molecular dynamics in the browser using LAMMPS
aromanro/SolarSystem
A solar system simulator with Verlet, using OpenGL for displaying.
wolberlab/pyrod
PyRod - Tracing water molecules in molecular dynamics simulations
choderalab/ensembler
Automated omics-scale protein modeling and simulation setup.
Mantevo/miniMD
MiniMD Molecular Dynamics Mini-App
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.
protocaller/ProtoCaller
Full automation of relative protein-ligand binding free energy calculations in GROMACS
d-SEAMS/seams-core
The d-SEAMS C++ core engine
smparker/molecular-blender
blend molecules!
pritampanda15/Molecular-Dynamics
Self explained tutorial for molecular dynamics simulation using gromacs
yesint/molar
Repository for molar crate and its dependencies
LABIOQUIM/visualdynamics
Web Platform made with Python and NextJS for automating GROMACS simulations
Mjolnir-MD/Mjolnir
:zap: general purpose coarse-grained molecular dynamics simulation package
MDAnalysis/membrane-curvature
MDAnalysis tool to calculate membrane curvature.
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)
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.
MolSSI/covid
MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store
datreant/MDSynthesis
a logistics and persistence engine for the analysis of molecular dynamics trajectories
Becksteinlab/propkatraj
pKa estimates for proteins using an ensemble approach