molecular-dynamics-simulation
There are 357 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.
theochem/iodata
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
SciML/NBodySimulator.jl
A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics
SENPAI-Molecular-Dynamics/SENPAI
Molecular dynamics simulation software
lammpstutorials/lammpstutorials.github.io
LAMMPS tutorials for both beginners and advanced users
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
timkartar/DeepPBS
Geometric deep learning of protein–DNA binding specificity
andeplane/atomify
Real time molecular dynamics in the browser using LAMMPS
aromanro/SolarSystem
A solar system simulator with Verlet, using OpenGL for displaying.
choderalab/ensembler
Automated omics-scale protein modeling and simulation setup.
wolberlab/pyrod
PyRod - Tracing water molecules in molecular dynamics simulations
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!
LABIOQUIM/visualdynamics
Web Platform made with Python and NextJS for automating GROMACS simulations
yesint/molar
Repository for molar crate and its dependencies
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)
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
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.
amirhajibabaei/AutoForce
Sparse Gaussian Process Potentials
HouGroup/mdgo
A codebase for classical molecular dynamics (MD) simulation setup and results analysis.