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Molecular Dynamics

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.

https://github.com/insilichem/tangram_mmsetup

A graphical interface to run OpenMM simulations in UCSF Chimera.

molecular-dynamics openmm ucsf-chimera

Last synced: 10 Nov 2024

https://github.com/liyigerry/gp120

Data, methods and code for research on the molecular dynamics of HIV glycoprotein gp120

gp120 markov-state-model molecular-dynamics simulation

Last synced: 05 Nov 2024

https://github.com/arm61/falass

Neutron and X-ray Reflectometry from Computer Simulation

molecular-dynamics molecular-dynamics-simulation neutron reflectivity reflectometry simulation x-ray

Last synced: 13 Nov 2024

https://github.com/mdsyn2019/research

PhD Molecular Dynamics Analysis Code - updated daily

chemistry molecular-dynamics molecular-modeling molecular-simulation

Last synced: 12 Oct 2024

https://github.com/klarh/hoomd_flowws

A library for modular HOOMD-Blue workflows

hoomd-blue molecular-dynamics molecular-simulation python simulation workflows

Last synced: 06 Nov 2024

https://github.com/kolaru/normalmodes.jl

Small utilities to deal with normal modes in molecular physics

molecular-dynamics molecule normal-modes

Last synced: 09 Oct 2024

https://github.com/simongravelle/thematic-school-soft-nanosciences-2023

LAMMPS simulations used during the 2023 thematic school

lammps molecular-dynamics school

Last synced: 08 Nov 2024

https://github.com/simongravelle/bash-tutorial

Efficiently handle multiple simulations using bash

bash lammps molecular-dynamics tutorial

Last synced: 08 Nov 2024

https://github.com/eschmidt42/singlecrystal.jl

Building single crystal structures easily

crystal molecular-dynamics notebook

Last synced: 08 Nov 2024

https://github.com/seatonullberg/lammps-trajectory-explorer

Bokeh dashboard to visualize LAMMPS trajectory files

bokeh lammps molecular-dynamics visualization

Last synced: 20 Oct 2024

https://github.com/simongravelle/mdanalysis-tutorial

Perform post-mortem analysis using Python and MDAnalysis

guide lammps mdanalysis molecular-dynamics tutorial

Last synced: 08 Nov 2024

https://github.com/ricalessandri/scattering

Simulated scattering patterns

giwaxs molecular-dynamics self-organization

Last synced: 12 Oct 2024

https://github.com/simongravelle/vmd-tutorial

Generate good-looking images and movies with VMD

guide lammps molecular-dynamics tutorials vmd

Last synced: 08 Nov 2024

https://github.com/babaid/aaperturb

A C++ library for the creation of a large dataset of amino acid sidechain perturbations, own PDB Parser code included and some other things related.

big-data gnn molecular-dynamics perturbation-methods structural-bioinformatics

Last synced: 08 Nov 2024

https://github.com/kneth/mdreac

Molecular Dynamics simulation coupled with chemical reactions

c chemical-reactions fortran molecular-dynamics

Last synced: 07 Nov 2024

https://github.com/toruniina/rustymill

MD toolbox written in rust

molecular-dynamics pdb rust science

Last synced: 20 Oct 2024

https://github.com/joaomcteixeira/dropped_taurenmd

An interface to streamline analisis routines for Molecular Dynamics.

molecular-dynamics molecular-dynamics-simulation python structural-biology

Last synced: 28 Oct 2024

https://github.com/evoyiatzis/intramolecularentropy

An implementation of Schlitter's quasi-harmonic approach to compute the intramolecular entropy of particle systems in python

molecular-dynamics

Last synced: 15 Oct 2024

https://github.com/jakublala/md-neural-ode

First two problems of my Master's Thesis on Coarse-Graining of Molecular Dynamics with Neural Ordinary Differential Equations

deep-learning machine-learning molecular-dynamics neural-ode toy-problems

Last synced: 07 Oct 2024

https://github.com/jakublala/coarsegrained-md-neural-ode

Thesis repository on neural ordinary differential equations used for coarse-graining molecular dynamics

coarse-grained-molecular-dynamics differential-equations molecular-dynamics neural-ode scientific-machine-learning thesis toy-problem

Last synced: 07 Oct 2024

https://github.com/janjoswig/cs-msm

Core-set Markov-state model estimation

core-set markov-model molecular-dynamics python

Last synced: 28 Oct 2024

https://github.com/xiaohanzhangcmu/axiom

scalable C++ and python binding framework for Scientific Computing and Machine Learning

deepq-learning finite-element-methods molecular-dynamics stanford tensorflow

Last synced: 28 Oct 2024

https://github.com/smahala02/atomistic-simulation

This project demonstrates how atomistic simulations are used to predict and analyze the behavior of atoms and molecules, providing detailed tutorials and simulations in a Jupyter Notebook.

atomistic-simulation computational-chemistry materials-science molecular-dynamics physics python

Last synced: 08 Nov 2024

https://github.com/simongravelle/lammpstutorials-old-solutions

Previous solution to the LAMMPS tutorials exercises

atomic lammps molecular-dynamics simulation

Last synced: 08 Nov 2024

https://github.com/snapex2409/komd

Small MD framework

kokkos md molecular-dynamics simulation

Last synced: 12 Oct 2024

https://github.com/toastisme/argon

A real-time MD toy allowing the user to play with both the pairwise and external potentials in a simulation of point particles

molecular-dynamics

Last synced: 10 Nov 2024

Molecular Dynamics Awesome Lists
awesome-python-chemistry 149 best-of-atomistic-machine-learning 296
Molecular Dynamics Categories
Interatomic Potentials (ML-IAP) 63 Representation Learning 42 General Tools 28 Language Models 24 Simulations 22 General Chemistry 19 Community resources 17 Representation Engineering 16 Datasets 15 Molecular Dynamics 14 Generative Models 13 Universal Potentials 11 Density functional theory (ML-DFT) 11 Visualization 10 Mathematical tools 10 Educational Resources 9 Molecular Visualization 8 Materials Discovery 7 Data Structures 7 Wavefunction methods (ML-WFT) 5