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: 111 MB - Last synced: about 2 hours ago - Pushed: about 3 hours ago - Stars: 11 - Forks: 12

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: 1.05 MB - Last synced: about 9 hours ago - Pushed: about 10 hours ago - Stars: 2 - Forks: 0

Smoren/molecular-ts

Virtual chemistry simultaion. Visualization of the behavior of particles in two-dimensional and three-dimensional space.

Language: TypeScript - Size: 29 MB - Last synced: about 3 hours ago - Pushed: about 16 hours ago - Stars: 16 - Forks: 0

Erastova-group/ClayCode

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

Language: Python - Size: 27.3 MB - Last synced: about 18 hours ago - Pushed: 1 day ago - Stars: 4 - Forks: 1

MDAnalysis/mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Language: Python - Size: 471 MB - Last synced: 1 day ago - Pushed: 6 days ago - Stars: 1,231 - Forks: 635

mlund/faunus

A Framework for Metropolis Monte Carlo Simulation of Molecular Systems

Language: C++ - Size: 39.2 MB - Last synced: about 7 hours ago - Pushed: 2 days ago - Stars: 66 - Forks: 33

openforcefield/openff-interchange

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

Language: Python - Size: 5.6 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 62 - Forks: 21

theochem/iodata

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

Language: Python - Size: 7.46 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 118 - Forks: 43

andeplane/atomify

Real time molecular dynamics in the browser using LAMMPS

Language: JavaScript - Size: 240 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 42 - Forks: 6

Acellera/moleculekit

MoleculeKit: Your favorite molecule manipulation kit

Language: Python - Size: 89.5 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 192 - Forks: 36

lanl/Architector

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

Language: Python - Size: 11.2 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 31 - Forks: 5

sreeharshab/scalar_codes

Codes for automating standard VASP and VASP-related calculations.

Language: Python - Size: 176 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 7 - Forks: 0

lumol-org/lumol

Universal extensible molecular simulation engine

Language: Rust - Size: 4.53 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 183 - Forks: 18

dgront/BioShell

Rust package for structure biology, bioinformatics and molecular modeling

Language: Rust - Size: 2.04 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 5 - Forks: 0

jparkhill/TensorMol

Tensorflow + Molecules = TensorMol

Language: Python - Size: 102 MB - Last synced: 9 days ago - Pushed: over 3 years ago - Stars: 269 - Forks: 74

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: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

nwchemgit/nwchem

NWChem: Open Source High-Performance Computational Chemistry

Language: Fortran - Size: 322 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 461 - Forks: 158

gxf1212/md-highlighter

a VScode syntax highlight tool for molecular dynamics

Size: 3.67 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 0 - Forks: 0

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: 8.3 MB - Last synced: 18 days ago - Pushed: about 2 months ago - Stars: 16 - Forks: 8

Smoren/molecular-python3

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

Language: Python - Size: 18.3 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 5 - Forks: 0

jvdhorn/decaf

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

Language: Python - Size: 440 KB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 2 - Forks: 0

rk-lindsey/chimes_calculator

Tools to interface ChIMES with various external codes.

Language: C++ - Size: 8.44 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 16 - Forks: 18

MolBioMedUAB/RCBS.py

RCBS.py (Reactivity of Chemical and Biochemical Systems) is a Python package that contains several scripts, functions and classes that simplify the analysis of chemical and biochemical simulations.

Language: Python - Size: 9.33 MB - Last synced: 25 days ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0

westpa/westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

Language: Python - Size: 19.8 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 181 - Forks: 48

aiqm/torchani

Accurate Neural Network Potential on PyTorch

Language: Python - Size: 74.1 MB - Last synced: 27 days ago - Pushed: about 2 months ago - Stars: 431 - Forks: 121

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: 28 days ago - Pushed: 2 months 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: 28 days ago - Pushed: 10 months ago - Stars: 10 - Forks: 1

andthum/mdtools

Scripts to prepare and analyze molecular dynamics simulations

Language: Python - Size: 12.7 MB - Last synced: 30 days ago - Pushed: about 1 month ago - Stars: 10 - Forks: 2

uibcdf/MolSysMT

Open source library to work with molecular systems

Language: Python - Size: 308 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 11 - Forks: 3

OpenBioSim/sire

Sire Molecular Simulations Framework

Language: C++ - Size: 79.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 33 - Forks: 7

Hori-Lab/SIS

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

Language: Fortran - Size: 1.08 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0

OpenBioSim/biosimspace

An interoperable Python framework for biomolecular simulation.

Language: Python - Size: 35 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 58 - Forks: 9

JuliaMolSim/Molly.jl

Molecular simulation in Julia

Language: Julia - Size: 81.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 361 - Forks: 51

shirtsgroup/physical_validation

Physical validation of molecular simulations

Language: Python - Size: 64.7 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 55 - Forks: 18

Institute-for-Future-Intelligence/aims

AIMS: Artificial Intelligence for Molecular Sciences

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

mosdef-hub/foyer

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

Language: Python - Size: 31.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 113 - Forks: 73

mosdef-hub/mbuild

A hierarchical, component based molecule builder

Language: Python - Size: 74.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 166 - Forks: 77

channotation/chap

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

Language: C++ - Size: 24.4 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 17 - Forks: 10

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: about 1 month ago - Pushed: about 1 month 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: about 2 months ago - Pushed: over 2 years ago - Stars: 10 - Forks: 12

openmm/openmm-tensorrt

OpenMM plugin to define forces with a TensorRT graph

Language: C++ - Size: 137 KB - Last synced: about 2 months ago - Pushed: about 4 years ago - Stars: 6 - Forks: 2

MaginnGroup/Cassandra

Cassandra is a Monte Carlo package to conduct atomistic simulations.

Language: Fortran - Size: 65.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 35 - Forks: 20

andthum/transfer_Li

Transfer Li ions from cathode to anode in MD simulations

Language: Shell - Size: 199 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

LoLab-MSM/PyBILT

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

Language: Python - Size: 31.3 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 24 - Forks: 10

daico007/surface_coatings

mBuild recipe to create different surface coating structure.

Language: Python - Size: 126 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 2 - Forks: 2

KULL-Centre/DEERpredict

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

Language: Jupyter Notebook - Size: 188 MB - Last synced: 27 days ago - Pushed: over 2 years ago - Stars: 8 - Forks: 3

m3g/ComplexMixtures.jl

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

Language: Julia - Size: 49.9 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 12 - Forks: 2

colbyford/HADDOCKer

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

Language: Shell - Size: 110 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 1

sarisabban/MiraMar

De novo cyclic protein polypeptide design using reinforcement learning.

Language: Python - Size: 2.26 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

rk-lindsey/chimes_lsq

Tools to develop ChIMES parameter sets

Language: DIGITAL Command Language - Size: 1.79 GB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 18

andrewtarzia/MCHammer

Implementation of cheap Monte Carlo optimisation of bonds in molecules

Language: Python - Size: 708 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 9 - Forks: 1

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: 2 months ago - Pushed: almost 6 years ago - Stars: 31 - Forks: 7

aqlaboratory/pnerf

Language: Python - Size: 60.5 KB - Last synced: 29 days ago - Pushed: almost 5 years ago - Stars: 34 - Forks: 6

poinco-gogo/md_alad

implementation of MD for TIP3P water simulation (faster)

Language: C++ - Size: 244 KB - Last synced: 3 months ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

poinco-gogo/md_analysis

Analysis tools for MD simulation

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

poinco-gogo/md_water

implementation of MD for TIP3P water simulation

Language: C++ - Size: 43 KB - Last synced: 3 months ago - Pushed: almost 5 years ago - Stars: 2 - 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: about 2 months ago - Pushed: 10 months ago - Stars: 11 - Forks: 4

andrewtarzia/CGExplore

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

Language: Python - Size: 2.31 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 1

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: 3 months ago - Pushed: over 5 years ago - Stars: 7 - Forks: 0

kimjc95/computational-chemistry

google colab codes to make computational chemistry easy

Language: Jupyter Notebook - Size: 19.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 4 - Forks: 0

harrydevnull/molecular-render

Language: HTML - Size: 213 KB - Last synced: 4 months ago - Pushed: over 6 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: 4 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 1

khavernathy/mcmd

Monte Carlo and Molecular Dynamics Simulation Package

Language: C++ - Size: 20.5 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 74 - Forks: 23

atoms-ufrj/EmDee

EmDee: A Molecular Dynamics Laboratory

Language: Fortran - Size: 932 KB - Last synced: 5 months ago - Pushed: over 5 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: 5 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

mindleaving/genome-tools

Tools for exploration and analysis of biochemical data like genomics and proteins

Language: C# - Size: 905 KB - Last synced: 5 months ago - Pushed: 11 months ago - Stars: 4 - Forks: 2

sarisabban/Pose

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

Language: Python - Size: 1.29 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 10 - Forks: 1

lmmentel/chemtools

Python tools for quantum chemical calculations

Language: Python - Size: 7.7 MB - Last synced: 23 days ago - Pushed: 4 months ago - Stars: 17 - Forks: 7

Ferg-Lab/integrin_molgen

Deep generative modeling of large multi-molecular systems

Language: Jupyter Notebook - Size: 313 MB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

timdecode/LifeBrush

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

Language: C++ - Size: 31.4 MB - Last synced: 2 months ago - Pushed: about 4 years ago - Stars: 49 - Forks: 8

lexin-chen/SciArt

aesthetic 3D images of biomolecules on Blender

Language: Tcl - Size: 34.3 MB - Last synced: about 1 month ago - Pushed: about 1 year 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: about 2 months ago - Pushed: almost 2 years ago - Stars: 13 - Forks: 23

kimjc95/addNewResidue.py

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

Language: Python - Size: 67.4 KB - Last synced: 5 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 2

gitesei/willard-chandler

Python-based tool to calculate instantaneous interfaces and concentration/orientation profiles from molecular simulation trajectories in slab geometry

Language: Jupyter Notebook - Size: 29.4 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 8 - Forks: 7

aiqm/aimnet

Atoms In Molecules Neural Network Potential

Language: Python - Size: 19 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 77 - Forks: 23

ekaakurniawan/hppNeuroDock

Molecular Docking Simulation Tool

Language: Python - Size: 34.6 MB - Last synced: 7 months ago - Pushed: almost 7 years ago - Stars: 3 - Forks: 3

nkkchem/CompMolNWChem

Language: Python - Size: 1.69 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 2

qusers/Q6

Q6 Repository -- EVB, FEP and LIE simulator.

Language: Fortran - Size: 33.9 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 30 - Forks: 16

Zhang-Zhiyuan-zzy/hotpot

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

Language: Python - Size: 4.37 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 11 - Forks: 1

lopesth/MoleKing_util

MoleKing_util is a Python module written in C++ with pybind11. This module contains several useful classes for those who program python scripts aimed at theoretical chemistry.

Language: C++ - Size: 1.5 MB - Last synced: 8 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

andrewtarzia/PoreMapper

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

Language: Python - Size: 505 KB - Last synced: 5 days ago - Pushed: 6 months ago - Stars: 7 - Forks: 1

uibcdf/OMembrane

Open source library to work with membranes

Language: Rich Text Format - Size: 633 MB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 1 - Forks: 2

mcolahan/mole-sim

Code for my PhD level molecular simulations class at Ohio University (CHE 7120)

Language: Jupyter Notebook - Size: 32.9 MB - Last synced: 8 months ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

juexinwang/NRI-MD

Neural relational inference for molecular dynamics simulations

Language: Python - Size: 13.1 MB - Last synced: 9 months ago - Pushed: 12 months ago - Stars: 26 - Forks: 12

Ferg-Lab/pines

Permutationally invariant networks for enhanced sampling (PINES)

Language: C++ - Size: 26.3 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

dquigley533/mc_water_ls_mw

Lattice-Switching Monte Carlo Code for the mW water model

Language: Fortran - Size: 215 KB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 2

ninjab3381/nmr_glycerol

Study of molecular motion of Glycerol using NMR modeling and simulations

Language: Python - Size: 32.3 MB - Last synced: 9 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

BSC-CNS-EAPM/AdaptivePELE

AdaptivePELE is a Python package aimed at enhancing the sampling of molecular simulations

Language: Python - Size: 34.8 MB - Last synced: 27 days ago - Pushed: 7 months ago - Stars: 14 - Forks: 13

kohnakagawa/LSCMD

A local stress calculation library for molecular dynamics simulations written in C++11

Language: C++ - Size: 57.6 KB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

klarh/hoomd_flowws

A library for modular HOOMD-Blue workflows

Language: Python - Size: 91.8 KB - Last synced: 10 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

klarh/flowws-examples

Example workflows using the flowws library

Language: Jupyter Notebook - Size: 13.7 KB - Last synced: 10 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

lyczak/MolecularPreloader 📦

📉 A 2D Maxwell Boltzmann distribution generator.

Language: F# - Size: 14.5 MB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

smlee99/InteractionGroup

Energy decomposition module for the analysis of molecular dynamics trajectories

Language: Python - Size: 434 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 0

Vikasdubey0551/svd_angle_between_vectors

'Fits' a vector/vectors to the helix/helicies using Singular Value Decomposition (SVD) and measures angle between them in a trajectory.

Language: Python - Size: 23.4 KB - Last synced: 10 months ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 0

dquigley533/hs_alkane

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

Language: Fortran - Size: 626 KB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 1

yagikiyoshi/sindo

A suite of programs for molecular vibrational analyses

Language: HTML - Size: 187 MB - Last synced: 10 months ago - Pushed: about 2 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: 4.31 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 6 - Forks: 2

achattaraj/maximal_Solubility_product

Python scripts to analyze and visualize the data presented in the research article: "The maximum solubility product marks the threshold for condensation of multivalent biomolecules".

Language: Jupyter Notebook - Size: 242 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

jmbr/go-replicants 📦

Molecular simulator for proteins that uses Go-type potentials

Language: C - Size: 278 KB - Last synced: about 1 year ago - Pushed: almost 13 years ago - Stars: 3 - Forks: 1

mlund/coulombgalore

C++ Library for Electrostatics

Language: C++ - Size: 543 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 10 - Forks: 4