An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: molecular-simulation

uibcdf/molsysmt

Open source library to work with molecular systems

Language: Python - Size: 379 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 13 - Forks: 3

aiqm/torchani

Accurate Neural Network Potential on PyTorch

Language: Python - Size: 82.9 MB - Last synced at: 1 day ago - Pushed at: 17 days ago - Stars: 509 - Forks: 138

mosdef-hub/msibi

A package for deriving coarse-grain potentials using MultiState Iterative Boltzmann Inversion (MS-IBI)

Language: Python - Size: 75.9 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 17 - Forks: 14

Acellera/moleculekit

MoleculeKit: Your favorite molecule manipulation kit

Language: Python - Size: 115 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 226 - Forks: 41

openforcefield/openff-interchange

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

Language: Python - Size: 6.68 MB - Last synced at: 1 day ago - Pushed at: 4 days ago - Stars: 79 - Forks: 25

pritampanda15/Molecular-Dynamics

Self explained tutorial for molecular dynamics simulation using gromacs

Language: Shell - Size: 30.8 MB - Last synced at: about 20 hours ago - Pushed at: 10 months ago - Stars: 28 - Forks: 14

mosdef-hub/mbuild

A hierarchical, component based molecule builder

Language: Python - Size: 74.8 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 198 - Forks: 81

mosdef-hub/foyer

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

Language: Python - Size: 31.7 MB - Last synced at: 1 day ago - Pushed at: 5 days ago - Stars: 133 - Forks: 77

nwchemgit/nwchem

NWChem: Open Source High-Performance Computational Chemistry

Language: Fortran - Size: 341 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 562 - Forks: 178

JuliaMolSim/Molly.jl

Molecular simulation in Julia

Language: Julia - Size: 88.2 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 444 - Forks: 58

dquigley533/hs_alkane

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

Language: Fortran - Size: 758 KB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 1 - Forks: 1

LierB/gromos_tutorial_livecoms Fork of biomos/gromos_tutorial_livecoms

Advanced tutorial for the GROMOS software for biomolecular simulation

Language: TeX - Size: 2.98 GB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 2

MDAnalysis/mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Language: Python - Size: 521 MB - Last synced at: 5 days ago - Pushed at: 16 days ago - Stars: 1,456 - Forks: 723

westpa/westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

Language: Python - Size: 34.2 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 203 - Forks: 58

h-brough/TUNA

A user-friendly quantum chemistry program for diatomics.

Language: Python - Size: 10.3 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 1 - Forks: 0

OpenBioSim/biosimspace

An interoperable Python framework for biomolecular simulation.

Language: Python - Size: 39.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 120 - Forks: 18

patrickallanfaustino/tutorials-md

Tutorials molecular dynamics.

Language: Makefile - Size: 6.2 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

patrickallanfaustino/patrickallanfaustino

Personal repo

Size: 1.51 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

M-c-tech-dev/mchammer

mchammer: a proof-of-concept for synthesizing hardware machine check exceptions (MCE) to explore processor exploitation, MCA analysis, and privilege escalation. 🔨

Size: 3.91 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

rk-lindsey/chimes_lsq

Tools to develop ChIMES parameter sets

Language: DIGITAL Command Language - Size: 2.26 GB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 2 - Forks: 25

andeplane/atomify

Real time molecular dynamics in the browser using LAMMPS

Language: C++ - Size: 244 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 61 - Forks: 10

Cavenfish/YASS.jl

Yet Another Simulation Suite (YASS.jl). A simulation suite for atomic simulations in Julia.

Language: Julia - Size: 13.1 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 0 - Forks: 0

JCelestial/molFrame

For when you are tired of writing new scripts for every Molecular Simulation

Language: Fortran - Size: 229 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0

Hori-Lab/UNISIS

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

Language: Fortran - Size: 1.31 MB - Last synced at: 3 days ago - Pushed at: 19 days ago - Stars: 4 - Forks: 1

OpenBioSim/sire

Sire Molecular Simulations Framework

Language: C++ - Size: 81.8 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 59 - Forks: 15

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 at: 21 days ago - Pushed at: almost 2 years ago - Stars: 15 - Forks: 13

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: 27 days ago - Pushed at: 27 days ago - Stars: 14 - Forks: 12

lanl/Architector

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

Language: Python - Size: 14.2 MB - Last synced at: 17 days ago - Pushed at: about 1 month ago - Stars: 64 - Forks: 14

Institute-for-Future-Intelligence/aims

AIMS: Artificial Intelligence for Molecular Sciences

Language: TypeScript - Size: 223 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 2

TheDisorderedOrganization/ParticlesMC

Package to run atomic / molecular Monte Carlo simulations

Language: Julia - Size: 63.2 MB - Last synced at: 1 day ago - Pushed at: 24 days ago - Stars: 18 - Forks: 0

lmmentel/chemtools

Python tools for quantum chemical calculations

Language: Python - Size: 7.7 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 19 - Forks: 7

justktln2/ciMIST

Network models of protein conformational entropy from dynamics

Language: Python - Size: 2.11 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

m3g/ComplexMixtures.jl

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

Language: Julia - Size: 60.9 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 20 - Forks: 3

khavernathy/mcmd

Monte Carlo and Molecular Dynamics Simulation Package

Language: C++ - Size: 20.5 MB - Last synced at: 6 days ago - Pushed at: about 1 year ago - Stars: 90 - Forks: 18

dgront/BioShell

Rust package for structure biology, bioinformatics and molecular modeling

Language: Rust - Size: 6.86 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 1

theochem/iodata

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

Language: Python - Size: 5.08 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 138 - Forks: 47

mlund/faunus

A Framework for Metropolis Monte Carlo Simulation of Molecular Systems

Language: C++ - Size: 39.1 MB - Last synced at: 1 day ago - Pushed at: about 2 months ago - Stars: 73 - Forks: 34

taka78/ultidock

An Autodock Vina automation project with basic data analysis tools.

Language: Python - Size: 468 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

yagikiyoshi/sindo

A suite of programs for molecular vibrational analyses

Language: HTML - Size: 190 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 1

timdecode/LifeBrush

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

Language: C++ - Size: 31.4 MB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 54 - Forks: 8

jparkhill/TensorMol

Tensorflow + Molecules = TensorMol

Language: Python - Size: 102 MB - Last synced at: 7 days ago - Pushed at: over 4 years ago - Stars: 275 - Forks: 72

jvdhorn/decaf

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

Language: Python - Size: 395 KB - Last synced at: 2 months ago - Pushed at: 2 months 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: 4.36 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 7 - Forks: 2

izgys/protein-stability-optimization

A computational pipeline for predicting stabilizing protein mutations using AI (ProteinMPNN) and validating their effects with molecular dynamics simulations.

Language: Python - Size: 5.89 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

IsabelThompson97/VersionControlled

Language: Python - Size: 32.8 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

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: 2 months ago - Pushed at: about 2 years ago - Stars: 14 - Forks: 3

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: 2 months ago - Pushed at: 2 months ago - Stars: 39 - Forks: 0

rk-lindsey/chimes_calculator

Tools to interface ChIMES with various external codes.

Language: C++ - Size: 49.7 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 22 - Forks: 28

lumol-org/lumol

Universal extensible molecular simulation engine

Language: Rust - Size: 4.53 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 198 - Forks: 19

aqlaboratory/pnerf

Language: Python - Size: 60.5 KB - Last synced at: 9 days ago - Pushed at: about 6 years ago - Stars: 36 - Forks: 5

DaoyuanLi2816/Molecule-Generator

Variational Autoencoder (VAE)-based molecular SMILES string generator

Language: Python - Size: 617 KB - Last synced at: about 3 hours ago - Pushed at: 5 months ago - Stars: 12 - Forks: 4

Killercavin/protein-binding

A protein binding and molecular screening platform

Language: TypeScript - Size: 1.22 MB - Last synced at: 27 days ago - Pushed at: 4 months ago - Stars: 0 - 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 at: about 2 months ago - Pushed at: over 4 years ago - Stars: 25 - Forks: 9

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: 4 months ago - Pushed at: 4 months 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 at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 1

gitesei/SI-peptidebilayer

Coarse-grained model of titrating peptides interacting with lipid bilayers

Language: Jupyter Notebook - Size: 7.19 MB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 0

rikedyp/APLPhys

Computational physics in APL

Language: Jupyter Notebook - Size: 8.75 MB - Last synced at: 16 days ago - Pushed at: over 5 years ago - Stars: 7 - Forks: 3

KULL-Centre/DEERpredict

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

Language: Jupyter Notebook - Size: 188 MB - Last synced at: 2 days ago - Pushed at: 4 months ago - Stars: 12 - Forks: 3

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: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

mlund/coulombgalore

C++ Library for Electrostatics

Language: C++ - Size: 573 KB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 16 - Forks: 4

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 at: 2 months ago - Pushed at: almost 6 years ago - Stars: 11 - Forks: 8

andrewtarzia/MCHammer

Implementation of cheap Monte Carlo optimisation of bonds in molecules

Language: Python - Size: 712 KB - Last synced at: 2 months ago - Pushed at: 12 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: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 1

DrugBud-Suite/CADD_Vault

Language: HTML - Size: 17.7 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 43 - Forks: 5

Smoren/molecular-python3

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

Language: Python - Size: 18.3 MB - Last synced at: 5 months ago - Pushed at: 9 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: 1.22 MB - Last synced at: 1 day ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0

andthum/transfer_Li

Transfer Li ions from cathode to anode in MD simulations

Language: Shell - Size: 201 KB - Last synced at: 2 days ago - Pushed at: 20 days ago - Stars: 2 - Forks: 0

andthum/mdtools

Scripts to prepare and analyze molecular dynamics simulations

Language: Python - Size: 12.7 MB - Last synced at: 2 days ago - Pushed at: 12 days ago - Stars: 9 - Forks: 2

sarisabban/Pose

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

Language: Python - Size: 1.32 MB - Last synced at: 2 days ago - Pushed at: 7 months ago - Stars: 16 - Forks: 3

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: 7 months ago - Pushed at: 7 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: 12 days ago - Pushed at: 7 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: 4 months 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: 38.4 MB - Last synced at: 18 days ago - Pushed at: 18 days 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: 2 days ago - Pushed at: 8 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: about 1 month ago - Pushed at: 8 months ago - Stars: 1 - Forks: 2

shirtsgroup/physical_validation

Physical validation of molecular simulations

Language: Python - Size: 64.7 MB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 56 - Forks: 20

mlund/SI-asynuclein-protonation

Supporting information for "Charge compensation during amyloid formation of alpha-synuclein"

Language: Jupyter Notebook - Size: 58.5 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

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: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 1

sarisabban/MiraMar

De novo cyclic protein polypeptide design using reinforcement learning.

Language: Python - Size: 2.26 MB - Last synced at: 11 months ago - Pushed at: 11 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: 10 months ago - Pushed at: about 3 years ago - Stars: 14 - Forks: 23

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: 11 months ago - Pushed at: 11 months ago - Stars: 18 - Forks: 9

kimjc95/addNewResidue.py

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

Language: Python - Size: 2.79 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 2

vtlim/plot_potential

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: about 2 months ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0

mlund/SI-thiocyanate

A Molecular Forcefield for Thiocyanate Anions in Water and at Interfaces

Language: HTML - Size: 81.8 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1

LeoGillet/chap-docker

CHAP Docker image source files

Language: Dockerfile - Size: 12.7 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

gxf1212/md-highlighter

a VScode syntax highlight tool for molecular dynamics

Size: 3.67 MB - Last synced at: over 1 year ago - Pushed at: over 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: 4 months ago - Pushed at: over 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: over 1 year ago - Pushed at: over 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: 2 days ago - Pushed at: 2 days ago - Stars: 10 - 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: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

MaginnGroup/Cassandra

Cassandra is a Monte Carlo package to conduct atomistic simulations.

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

daico007/surface_coatings

mBuild recipe to create different surface coating structure.

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

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: over 1 year ago - Pushed at: about 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: about 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: almost 4 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: about 6 years ago - Stars: 2 - Forks: 1

harrydevnull/molecular-render

Language: HTML - Size: 213 KB - Last synced at: over 1 year ago - Pushed at: about 8 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: almost 5 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: almost 7 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

Related Keywords
molecular-simulation 157 molecular-dynamics 76 computational-chemistry 29 molecular-dynamics-simulation 28 molecular-modeling 28 chemistry 24 python 23 quantum-chemistry 13 monte-carlo-simulation 12 computational-biology 11 gromacs 11 simulation 8 force-field 7 machine-learning 7 molecular-mechanics 6 protein-structure 6 openmm 6 materials-science 6 proteins 6 cheminformatics 6 monte-carlo 5 bioinformatics 5 drug-discovery 5 lammps 5 science 5 pdb 5 neural-network 5 mdanalysis 4 biophysics 4 physics-simulation 4 physics 4 computational-physics 4 biomolecular-simulation 4 scientific-computing 4 computational-science 4 numpy 4 molecule 4 forcefield 3 charmm 3 amber 3 namd 3 python-scripts 3 high-throughput 3 julia 3 molecules 3 atomistic-simulations 3 trajectory-analysis 3 quantum-mechanics 3 cpp 3 free-energy-calculations 3 molecular-structures 3 reproducible-research 3 graph-neural-networks 3 deep-learning 3 visualization 2 physical-chemistry 2 canvas 2 machine-learning-force-field 2 optimization-algorithms 2 python3 2 genomics 2 thermodynamics 2 chemoinformatics 2 chemical-engineering 2 denovo-design 2 ion-channel 2 pytorch 2 chemistry-molecule 2 protein-design 2 kinetic-monte-carlo 2 docking 2 ligand-screening 2 nmr-spectroscopy 2 statistical-mechanics 2 xyz 2 spectroscopy 2 crystal 2 molecular-biology 2 scipy 2 insilico 2 ai 2 reinforcement-learning 2 qmmm 2 pca 2 interoperability 2 coarse-graining 2 parallel-computing 2 mbuild 2 coarse-grained-molecular-dynamics 2 molsysmt 2 monte-carlo-sampling 2 md-simulations 2 workflows 2 mosdef 2 modeling 2 high-performance-computing 2 lennard-jones 2 quantum-chemistry-programs 2 theoretical-chemistry 2 molecular-dynamics-trajectories 2