https://github.com/gnikit/md-sim

A mesh free molecular dynamics (MD) simulation for a fluid in an isothermal container

coarse-grained-molecular-dynamics fluid fluid-simulation md-simulations molecular-dynamics

Last synced: 15 Oct 2024

https://github.com/pjaselin/studio_lammps

Interactive dashboard-style interface to LAMMPS

education lammps molecular-dynamics plotly python r reticulate shiny shiny-server

Last synced: 14 Oct 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/simongravelle/simongravelle

README file for Github profile

github inkscape molecular-dynamics

Last synced: 08 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/simongravelle/bash-tutorial

Efficiently handle multiple simulations using bash

bash lammps molecular-dynamics tutorial

Last synced: 08 Nov 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/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/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/toruniina/trajan

trajectory analysis

molecular-dynamics science trajectory-analysis

Last synced: 20 Oct 2024

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

Building single crystal structures easily

crystal molecular-dynamics notebook

Last synced: 08 Nov 2024

https://github.com/kevinshen56714/polymer-molecular-dynamics

Modern, fast, python framework for building LAMMPS input and data files for predicting polymer properties

computing computing-framework data-science high-performance-computing informatics lammps lammps-data lammps-input machine-learning machine-learning-pipelines materials-informatics molecular-dynamics molecular-dynamics-simulation polymer pypi pypi-package python python-library python3 simulations

Last synced: 02 Oct 2024

https://github.com/ricalessandri/scattering

Simulated scattering patterns

giwaxs molecular-dynamics self-organization

Last synced: 12 Oct 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/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/kneth/mdreac

Molecular Dynamics simulation coupled with chemical reactions

c chemical-reactions fortran molecular-dynamics

Last synced: 07 Nov 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

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/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/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/diegonti/md_simulation

EIA Project for the Computational Modelling Master's Degree.

fortran lennard-jones molecular-dynamics mpi multiprocessing parallel-computing

Last synced: 14 Nov 2024

https://github.com/klarh/flowws-examples

Example workflows using the flowws library

examples molecular-dynamics molecular-simulation notebook python simulation visualization workflows

Last synced: 06 Nov 2024

https://github.com/ricalessandri/polyp3ht

Polymerize Atomistic P3HT

atomistic force-fields molecular-dynamics polymers

Last synced: 12 Oct 2024

https://github.com/singularitti/moleculardynamics.jl

A simple molecular dynamics demo using Julia

julia julia-package materials-science metropolis-hastings molecular-dynamics molecular-dynamics-simulation monte-carlo-simulation physics-simulation

Last synced: 06 Nov 2024

https://github.com/diegonti/momo

Practical Sessions problems for the Molecular Modelling course of the "Atomistic and Multiscale Computational Modelling" Master Degree. Course 2022-2023.

computational-chemistry molecular-dynamics molecular-modelling montecarlo-simulation

Last synced: 14 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/toruniina/rustymill

MD toolbox written in rust

molecular-dynamics pdb rust science

Last synced: 20 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/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/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/insilichem/tangram_dummyatoms

graphical-interface molecular-dynamics ucsf-chimera

Last synced: 10 Nov 2024