GitHub topics: molecular-simulation

Repositories

nwchemgit/nwchem

NWChem: Open Source High-Performance Computational Chemistry

Language: Fortran - Size: 341 MB - Last synced at: about 11 hours ago - Pushed at: about 12 hours ago - Stars: 540 - Forks: 172

theochem/iodata

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

Language: Python - Size: 5.07 MB - Last synced at: about 4 hours ago - Pushed at: 2 months ago - Stars: 137 - Forks: 48

mosdef-hub/mbuild

A hierarchical, component based molecule builder

Language: Python - Size: 74.7 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 192 - Forks: 82

openforcefield/openff-interchange

A project (and object) for storing, manipulating, and converting molecular mechanics data.

Language: Python - Size: 6.35 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 75 - Forks: 24

MDAnalysis/mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Language: Python - Size: 511 MB - Last synced at: 1 day ago - Pushed at: 5 days ago - Stars: 1,423 - Forks: 711

jvdhorn/decaf

A Python package for extracting and simulating diffuse scattering of X-rays in protein crystals

Language: Python - Size: 551 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 3 - Forks: 0

taka78/ultidock

An Autodock Vina automation project with basic data analysis tools.

Language: Python - Size: 450 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

Acellera/moleculekit

MoleculeKit: Your favorite molecule manipulation kit

Language: Python - Size: 112 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 219 - Forks: 37

dgront/BioShell

Rust package for structure biology, bioinformatics and molecular modeling

Language: Rust - Size: 6.83 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 7 - Forks: 0

JuliaMolSim/Molly.jl

Molecular simulation in Julia

Language: Julia - Size: 83.9 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 427 - Forks: 58

Killercavin/protein-binding

A protein binding and molecular screening platform

Language: TypeScript - Size: 1.22 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

KULL-Centre/DEERpredict

Software for the prediction of DEER and PRE data from conformational ensembles.

Language: Jupyter Notebook - Size: 188 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 12 - Forks: 3

mosdef-hub/foyer

A package for atom-typing as well as applying and disseminating forcefields

Language: Python - Size: 31.6 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 128 - Forks: 78

dquigley533/hs_alkane

Fortran2003 code (with C and Python bindings) implementing hard-sphere alkane models

Language: Fortran - Size: 681 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 1 - Forks: 1

jparkhill/TensorMol

Tensorflow + Molecules = TensorMol

Language: Python - Size: 102 MB - Last synced at: 10 days ago - Pushed at: over 4 years ago - Stars: 273 - Forks: 73

archettialberto/commence-tmbc

A preliminary study of emergent molecular communication protocols learned by graph-based agents in a diffusion channel environment.

Language: Jupyter Notebook - Size: 112 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

westpa/westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

Language: Python - Size: 46.7 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 199 - Forks: 57

khavernathy/mcmd

Monte Carlo and Molecular Dynamics Simulation Package

Language: C++ - Size: 20.5 MB - Last synced at: 1 day ago - Pushed at: 10 months ago - Stars: 86 - Forks: 19

lanl/Architector

The architector python package - for 3D metal complex design. C22085

Language: Python - Size: 14.1 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 45 - Forks: 8

DaoyuanLi2816/Molecule-Generator

Variational Autoencoder (VAE)-based molecular SMILES string generator

Language: Python - Size: 617 KB - Last synced at: 6 days ago - Pushed at: 21 days ago - Stars: 11 - Forks: 2

uibcdf/molsysmt

Open source library to work with molecular systems

Language: Python - Size: 373 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 13 - Forks: 3

wisecashew/suite

This is a large set of programs that runs and analyzes lattice simulations. For a more contained version of MCLattE, please visit the repo linked below.

Language: C++ - Size: 1.29 GB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 0 - Forks: 0

OpenBioSim/sire

Sire Molecular Simulations Framework

Language: C++ - Size: 81 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 52 - Forks: 14

lumol-org/lumol

Universal extensible molecular simulation engine

Language: Rust - Size: 4.53 MB - Last synced at: 16 days ago - Pushed at: over 1 year ago - Stars: 196 - Forks: 18

etomica/etomica

Etomica is a molecular simulation framework written in Java, developed at the Department of Chemical & Biological Engineering at the University at Buffalo.

Language: Java - Size: 112 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 13 - Forks: 12

pritampanda15/Molecular-Dynamics

Self explained tutorial for molecular dynamics simulation using gromacs

Language: Shell - Size: 30.8 MB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 23 - Forks: 11

Smoren/molecular-ts

Virtual chemistry simultaion. Particle automata. Visualization of the behavior of particles in 2D and 3D space. Artifical life research.

Language: TypeScript - Size: 29.8 MB - Last synced at: 29 days ago - Pushed at: about 1 month ago - Stars: 37 - Forks: 0

andrewtarzia/PoreMapper

cavity shape and size mapping by growing a guest inside a host

Language: Python - Size: 505 KB - Last synced at: 24 days ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 1

andeplane/atomify

Real time molecular dynamics in the browser using LAMMPS

Language: C++ - Size: 243 MB - Last synced at: 25 days ago - Pushed at: about 2 months ago - Stars: 55 - Forks: 8

andrewtarzia/MCHammer

Implementation of cheap Monte Carlo optimisation of bonds in molecules

Language: Python - Size: 712 KB - Last synced at: 11 days ago - Pushed at: 8 months ago - Stars: 10 - Forks: 1

LESC-Unicamp/Monte-Carlo-Mixtures-of-Ellipsoids-Spherocylinders-Cylinders

This is a NVT/NPT-Monte Carlo algorithm designed to evaluate the thermodynamic behavior of mixtures of some hard convex bodies: ellipsoids of revolution, spherocylinders, and cylinders.

Language: Fortran - Size: 1020 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 1

aiqm/torchani

Accurate Neural Network Potential on PyTorch

Language: Python - Size: 74.1 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 487 - Forks: 137

DrugBud-Suite/CADD_Vault

Language: HTML - Size: 17.7 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 43 - Forks: 5

mlund/faunus

A Framework for Metropolis Monte Carlo Simulation of Molecular Systems

Language: C++ - Size: 39.1 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 70 - Forks: 34

m3g/ComplexMixtures.jl

Package to perform minimum-distance distribution analyses of complex solute-solvent interactions

Language: Julia - Size: 59.8 MB - Last synced at: 20 days ago - Pushed at: 2 months ago - Stars: 17 - Forks: 3

Smoren/molecular-python3

Virtual chemistry simulation in 2D based on numpy and numba.

Language: Python - Size: 18.3 MB - Last synced at: 29 days ago - Pushed at: 5 months ago - Stars: 9 - Forks: 0

andthum/lintf2_ether_ana_postproc

Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures

Language: Python - Size: 1.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

andthum/transfer_Li

Transfer Li ions from cathode to anode in MD simulations

Language: Shell - Size: 200 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

andthum/mdtools

Scripts to prepare and analyze molecular dynamics simulations

Language: Python - Size: 12.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 2

IsabelThompson97/VersionControlled

Language: Jupyter Notebook - Size: 16.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

sarisabban/Pose

A bare metal Python library for building and manipulating protein molecular structures

Language: Python - Size: 1.32 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 16 - Forks: 3

yagikiyoshi/sindo

A suite of programs for molecular vibrational analyses

Language: HTML - Size: 190 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1

Erastova-group/ClayCode

automate the setup of atomistic clay models for classical molecular dynamics simulations with GROMACS

Language: Python - Size: 27.9 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 7 - Forks: 2

andrewtarzia/CGExplore

A general tool set for working with coarse-grained stk models

Language: Python - Size: 5.95 MB - Last synced at: 24 days ago - Pushed at: 3 months ago - Stars: 1 - Forks: 1

channotation/chap

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

Language: C++ - Size: 24.4 MB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 10

Zhang-Zhiyuan-zzy/hotpot

A python package designed to communicate among various chemical and materials calculational tools

Language: Python - Size: 37.2 MB - Last synced at: about 5 hours ago - Pushed at: about 6 hours ago - Stars: 11 - Forks: 1

sreeharshab/scalar_codes

Codes for automating standard VASP and VASP-related calculations.

Language: Python - Size: 3.48 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 8 - Forks: 1

uibcdf/OMembrane

Open source library to work with membranes

Language: Rich Text Format - Size: 644 MB - Last synced at: 28 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 2

shirtsgroup/physical_validation

Physical validation of molecular simulations

Language: Python - Size: 64.7 MB - Last synced at: about 10 hours ago - Pushed at: about 1 month ago - Stars: 56 - Forks: 20

Hori-Lab/SIS

Coarse-grained molecular dynamics simulation with the Single-Interaction-Site RNA model

Language: Fortran - Size: 1.23 MB - Last synced at: 5 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 0

timdecode/LifeBrush

A toolkit for painting agent-based mesoscale molecular simulations and illustrations.

Language: C++ - Size: 31.4 MB - Last synced at: 6 months ago - Pushed at: about 5 years ago - Stars: 53 - Forks: 8

colbyford/HADDOCKer

Docker images for the running the HADDOCK system for predicting the structure of biomolecular complexes.

Language: Shell - Size: 110 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

yuyangw/Denoise-Pretrain-ML-Potential

Implementation of "Denoise Pretraining on Non-equilibrium Molecular Conformations for Accurate and Transferable Neural Potentials" in PyTorch.

Language: Python - Size: 31.8 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 13 - Forks: 3

mlund/coulombgalore

C++ Library for Electrostatics

Language: C++ - Size: 549 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 14 - Forks: 4

OpenBioSim/biosimspace

An interoperable Python framework for biomolecular simulation.

Language: Python - Size: 38.7 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 75 - Forks: 11

sarisabban/MiraMar

De novo cyclic protein polypeptide design using reinforcement learning.

Language: Python - Size: 2.26 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0

mosdef-hub/mosdef-workflows

Sample molecular simulation workflows using a MoSDeF and community tools

Language: Jupyter Notebook - Size: 1.51 MB - Last synced at: 7 months ago - Pushed at: almost 3 years ago - Stars: 14 - Forks: 23

aqlaboratory/pnerf

Language: Python - Size: 60.5 KB - Last synced at: 19 days ago - Pushed at: almost 6 years ago - Stars: 35 - Forks: 5

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.

Language: Python - Size: 9.16 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 18 - Forks: 9

rikedyp/APLPhys

Computational physics in APL

Language: Jupyter Notebook - Size: 8.75 MB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 3

kimjc95/addNewResidue.py

This code adds custom-made amino acids to the GROMACS forcefield directory.

Language: Python - Size: 2.79 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 8 - Forks: 2

Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.

Language: Python - Size: 186 KB - Last synced at: 2 months ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 0

vpasumarthi/PyCD

Open-source, cross-platform application supporting lattice-based kinetic Monte Carlo simulations in crystalline systems

Language: Python - Size: 4.32 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 7 - Forks: 2

LeoGillet/chap-docker

CHAP Docker image source files

Language: Dockerfile - Size: 12.7 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

rk-lindsey/chimes_calculator

Tools to interface ChIMES with various external codes.

Language: C++ - Size: 8.63 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 17 - Forks: 19

gxf1212/md-highlighter

a VScode syntax highlight tool for molecular dynamics

Size: 3.67 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

saifaldin14/Molecular-Chemistry-Visualization

A Unity program to identify the VSPER shape of a molecular compound. Custom C++ backend library to identify the shapes of the molecules and a Unity C# frontend

Language: C++ - Size: 2.13 MB - Last synced at: 18 days ago - Pushed at: about 6 years ago - Stars: 8 - Forks: 0

lujiarui/Str2Str

Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)

Language: Python - Size: 979 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 49 - Forks: 0

keithgroup/mbGDML

Create, use, and analyze machine learning potentials within the many-body expansion framework.

Language: Python - Size: 47.4 MB - Last synced at: 23 days ago - Pushed at: almost 2 years ago - Stars: 10 - Forks: 1

Institute-for-Future-Intelligence/aims

AIMS: Artificial Intelligence for Molecular Sciences

Language: JavaScript - Size: 84 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 1

schulz-helena/soliton-implementation

Repository for my bachelor thesis and consecutive research on the soliton automata model

Language: Python - Size: 7.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

mosdef-hub/msibi

A package for managing pair-potential derivation using MultiState Iterative Boltzmann Inversion (MS-IBI)

Language: Python - Size: 25.4 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 12

MaginnGroup/Cassandra

Cassandra is a Monte Carlo package to conduct atomistic simulations.

Language: Fortran - Size: 65.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 35 - Forks: 20

LoLab-MSM/PyBILT

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

Language: Python - Size: 31.3 MB - Last synced at: 6 days ago - Pushed at: about 4 years ago - Stars: 24 - Forks: 9

daico007/surface_coatings

mBuild recipe to create different surface coating structure.

Language: Python - Size: 126 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 2

rk-lindsey/chimes_lsq

Tools to develop ChIMES parameter sets

Language: DIGITAL Command Language - Size: 1.79 GB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 18

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.

Size: 7.28 MB - Last synced at: about 1 year ago - Pushed at: almost 7 years ago - Stars: 31 - Forks: 7

poinco-gogo/md_alad

implementation of MD for TIP3P water simulation (faster)

Language: C++ - Size: 244 KB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

poinco-gogo/md_analysis

Analysis tools for MD simulation

Language: C++ - Size: 313 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

poinco-gogo/md_water

implementation of MD for TIP3P water simulation

Language: C++ - Size: 43 KB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 1

harrydevnull/molecular-render

Language: HTML - Size: 213 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

b-tudor/mpmcxx

MPMC++ | This is the MPMC (github.com/mpmccode/mpmc) molecular simulator rewritten in C++ in order to add the ability to integrate Feynman Path Integrals and "multi-system" stat mech ensembles (e.g. Gibbs).

Language: C++ - Size: 1.91 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1

atoms-ufrj/EmDee

EmDee: A Molecular Dynamics Laboratory

Language: Fortran - Size: 932 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 5

lucasboistay/molecular_dynamics

This project involves utilizing results from ab initio molecular dynamics simulations to develop a model capable of predicting the energy associated with specific molecular configurations. It leverages two datasets of configurations and energies for different molecules : Zundel ion (H2O-H-H2O) and Molybdenum-Sulfur aggregate (Mo2S4).

Language: Jupyter Notebook - Size: 29.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0