The Wayback Machine - https://web.archive.org/web/20210823211637/https://github.com/topics/molecular-dynamics-simulation

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molecular-dynamics-simulation

Molecular dynamics allows the atoms and molecules to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system.

Here are 155 public repositories matching this topic...

MDAnalysis / mdanalysis

Star

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

python science molecular-dynamics computational-chemistry molecular-simulation molecular-dynamics-simulation trajectory-analysis mdanalysis

Updated Aug 22, 2021
Python

brucefan1983 / CUDA-Programming

Star

Sample codes for my CUDA programming book

molecular-dynamics-simulation gpu-programming cuda-programming

Updated Mar 18, 2021
Cuda

choderalab / yank

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An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

python molecular-dynamics openmm molecular-dynamics-simulation drug-discovery free-energy free-energy-perturbation alchemical-free-energy-calculations mskcc alchemical

Updated Nov 15, 2020
Python

senpai

Chelsea486MHz / senpai

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Open

Translation (German, French, Spanish, Italian...)

4

Chelsea486MHz commented Jul 20, 2021

Objective

Provide a German translation of the strings defined in headers/text.h.

Rationale

Users, especially in educative contexts, might want to use the software in their native language.

Read more

enhancement help wanted good first issue

Open

Implement bond torsion

SciML / NBodySimulator.jl

Sponsor Star

A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics

automatic-differentiation molecular-dynamics molecular-dynamics-simulation geometric-algorithms algorithmic-differentiation differentiable-programming symbolic-integration scientific-machine-learning sciml

Updated May 5, 2021
Julia

brucefan1983 / GPUMD

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Graphics Processing Units Molecular Dynamics

gpu cuda molecular-dynamics molecular-dynamics-simulation phonon heat-transport gpumd

Updated Aug 13, 2021
Cuda

MobleyLab / drug-computing

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Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.

python monte-carlo molecular-dynamics solubility molecular-dynamics-simulation drug-discovery docking ligand-screening teaching-materials educational-software

Updated Mar 5, 2020
HTML

theochem / iodata

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Python library for reading, writing, and converting computational chemistry file formats and generating input files.

json-schema molecular-dynamics computational-biology computational-chemistry molecular-simulation computational-physics molecular-dynamics-simulation file-converter quantum-chemistry file-conversion quantum-chemistry-programs data-parsing molecular-mechanics input-output file-format-converter file-formats theoretical-chemistry file-format-library quantum-chemistry-packages molecular-electronic-structure

Updated Aug 12, 2021
Python

khavernathy / mcmd

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Monte Carlo and Molecular Dynamics Simulation Package

crystal chemistry atomic pdb physics monte-carlo molecular-dynamics molecular-simulation molecular-dynamics-simulation monte-carlo-simulation crystal-structure physics-simulation molecules monte-carlo-simulations gas-model gas-dynamics xyz periodicity polarization nvt

Updated Apr 21, 2021
C++

choderalab / ensembler

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Automated omics-scale protein modeling and simulation setup.

python molecular-dynamics-simulation homology-modeling modeller superfamily

Updated Dec 31, 2016
Python

aromanro / SolarSystem

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A solar system simulator with velocity Verlet, using OpenGL for displaying.

opengl lightning shaders xml physics planet molecular-dynamics moon computational-physics molecular-dynamics-simulation solar gravitation glm physics-simulation solarsystem mfc shadow gravitational-simulations

Updated Feb 8, 2021
C++

datreant / MDSynthesis

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a logistics and persistence engine for the analysis of molecular dynamics trajectories

python science database molecular-dynamics-simulation mdanalysis

Updated Jan 24, 2020
Python

MolSSI / covid

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MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store

molecular-dynamics molecular-dynamics-simulation md-simulations covid-19 sars-cov-2 covid19-data

Updated Aug 12, 2021
HTML

schallerdavid / pyrod

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PyRod - Tracing water molecules in molecular dynamics simulations

python3 molecular-dynamics-simulation water pharmacophore

Updated Jan 5, 2021
Python

protocaller / ProtoCaller

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Full automation of relative protein-ligand binding free energy calculations in GROMACS

python molecular-dynamics-simulation high-throughput gromacs free-energies ligand-binding

Updated May 3, 2021
Python

m3g / CellListMap.jl

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Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbour lists, etc.

molecular-dynamics molecular-dynamics-simulation minimum-distances

Updated Aug 20, 2021
Julia

Mjolnir-MD / Mjolnir

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⚡ general purpose coarse-grained molecular dynamics simulation package

science c-plus-plus simulation c-plus-plus-11 openmp molecular-dynamics-simulation coarse-grained

Updated Aug 19, 2021
C++

seams-core

d-SEAMS / seams-core

Star

Open

Add coverage metrics

HaoZeke commented Mar 12, 2020

Is your feature request related to a problem? Please describe.
Currently it is difficult to keep track of which tests are present and which should be implemented.
Describe the solution you'd like

Given that it is a C++ project, it makes sense to use lcov

Read more

enhancement good first issue todo 🗒️

LoLab-VU / PyBILT

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Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.

molecular-simulation molecular-dynamics-simulation analyses molecular-dynamics-trajectories lipids lipid-bilayers

Updated May 12, 2021
Python

markovmodel / adaptivemd

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A python framework to run adaptive Markov state model (MSM) simulation on HPC resources

python markov-model hpc molecular-dynamics-simulation adaptive

Updated Sep 13, 2019
Python

aromanro / EventMolecularDynamics

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A program implementing event driven molecular dynamics for hard smooth spheres, using OpenGL for displaying

opengl lightning simulation shaders physics sphere molecular-dynamics collision particles computational-physics molecular-dynamics-simulation event-driven glm mfc

Updated Nov 18, 2020
C++

ls1mardyn / ls1-mardyn

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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.

simulation molecular-dynamics scientific-computing molecular-dynamics-simulation ls1-mardyn nanofluidics autopas

Updated Jul 28, 2021
C++

leelasd / ligpargen

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A repository for tutorials and FAQ's about LigParGen

molecular-dynamics-simulation force-field ligpargen-server opls-aa

Updated Aug 12, 2018
Python

Becksteinlab / propkatraj

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pKa estimates for proteins using an ensemble approach

molecular-dynamics-simulation mdanalysis pka-predictions

Updated Jul 14, 2020
Python

MDAnalysis / pytng

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Python bindings for TNG file format

file-format molecular-dynamics-simulation gromacs trajectory

Updated Apr 23, 2021
C

channotation / chap

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CHAP is a tool for the functional annotation of ion channel structures:

molecular-dynamics molecular-simulation molecular-dynamics-simulation ion-channel

Updated Jul 12, 2021
C++

RUBi-ZA / MODE-TASK

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PCA and normal mode analysis of proteins

python pdb molecular-dynamics protein molecular-dynamics-simulation mds trajectory-analysis tsne principal-component-analysis rmsd normal-modes

Updated Aug 17, 2021
C++

jaantollander / CellLists.jl

Sponsor Star

Julia language implementation of the Cell Lists algorithm to solve the fixed-radius near neighbors problem including serial and multithreaded algorithms.

julia molecular-dynamics-simulation agent-based-simulation fixed-radius-near-neighbors cell-lists

Updated Aug 21, 2021
Julia

MDAnalysis / membrane-curvature

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MDAnalysis tool to calculate membrane curvature.

python molecular-dynamics-simulation trajectory-analysis mdanalysis

Updated Aug 21, 2021
Python

igemsoftware2020 / Hannover

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This repository contains the code for simulating the growth of a Biofilm after attachment using Molecular dynamics simulation methods. The project was build as part of the iGEM 2020 Contest. The BiofilmSimulation software can be installed as A python package, documented under https://pypi.org/project/BiofilmSimulation.

molecular-dynamics-simulation software-tools igem-competition biofilm-growth

Updated May 21, 2021
Jupyter Notebook

Wikipedia: Wikipedia

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