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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/conorwilliams/openfly

The open framework for on-the-fly off-lattice kinetic Monte Carlo simulations.

kinetic-monte-carlo molecular-dynamics off-lattice-model on-the-fly particle-simulation simulation

Last synced: 20 Nov 2024

https://github.com/llnl/ezalign

Coarse grain to atomistic molecular coordinate and topology converter

biology molecular-dynamics

Last synced: 11 Nov 2024

https://github.com/sbischoff-ai/simple-molecular-dynamics

Some C++ code for basic Molecular Dynamics simulations.

molecular-dynamics physics simulation velocity-verlet

Last synced: 08 Dec 2024

https://github.com/ur-whitelab/peptidesim

Automated peptide simulation tool with gromacs, gromacswrapper, plumed

gromacs molecular-dynamics peptides

Last synced: 23 Nov 2024

https://github.com/jdrusso/msm_we

History-augmented Markov analysis of weighted ensemble trajectories.

markov-model molecular-dynamics weighted-ensemble

Last synced: 13 Nov 2024

https://github.com/uibcdf/academia

Este repositorio debe ser el punto de partida y encuentro para cualquier investigador o estudiante que quiera comenzar a trabajar con/en la UIBCDF. Si has caído aquí por otro motivo y este material te es útil, eres más que bienvenido a usarlo e interaccionar con nosotros.

academic-project cc-by-sa conda drug-design drug-discovery git github jupyter molecular-dynamics molecular-dynamics-simulation python spanish-language tutorials

Last synced: 22 Nov 2024

https://github.com/becksteinlab/zarrtraj

zarrtraj MDAKit for @MDAnalysis

file-format mdanalysis molecular-dynamics streaming zarr

Last synced: 10 Nov 2024

https://github.com/li012589/xyzFile2Animation

A small python script to create animation from multiply xyz files

animation molecular-dynamics xyz xyz-files

Last synced: 23 Nov 2024

https://github.com/yesint/molar

Repository for molar crate and its dependencies

molecular-dynamics molecular-dynamics-simulation molecular-modeling trajectory-analysis

Last synced: 26 Nov 2024

https://github.com/allisterb/onemd

Data-parallel molecular dynamics simulator for Intel oneAPI.

cpp cpp17 devcloud dpcpp intel molecular-dynamics simulation

Last synced: 07 Nov 2024

https://github.com/sizmailov/pyxmolpp2

Processing and analysis of MD trajectories

analysis cxx md molecular-dynamics pdb python

Last synced: 09 Nov 2024

https://github.com/bartbruininks/mdvcontainment

Robust characterization of inside and outside in periodic spaces.

containment graph md molecular-dynamics point-cloud segmentation topology visualization voxels

Last synced: 10 Nov 2024

https://github.com/ricalessandri/martini3-mappings

Mapping small-molecules to Martini 3 coarse-grained representations

coarse-graining martini3 molecular-dynamics

Last synced: 19 Nov 2024

https://github.com/petercollingridge/atomic.js

A Javascript library for building simple atomic simulations.

canvas chemistry javascript molecular-dynamics simulation

Last synced: 06 Dec 2024

https://github.com/jbarnoud/simoji

Run a GROMACS simulation with emojis!

emoji gromacs molecular-dynamics

Last synced: 06 Nov 2024

https://github.com/chiang-yuan/muse

A python package for fast building amorphous solids and liquid mixtures from @materialsproject computed structures and machine learning interatomic potentials

atomistic-simulations high-throughput interatomic-potentials machine-learning materials molecular-dynamics

Last synced: 18 Dec 2024

https://github.com/njzjz/kconmd

Molecular dynamics (MD) simulations supported by k-Bags Convolutional Neural Network (kcon).

chemistry convolutional-neural-network deep-learning molecular-dynamics python3 tensorflow

Last synced: 28 Oct 2024

https://github.com/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.

computational-chemistry cosine coulomb-interactions energy-functions forcefield harmonic lennard-jones matplotlib molecular-dynamics molecular-modeling molecular-simulation morse potential presentation-materials vdw

Last synced: 18 Nov 2024

https://github.com/janjoswig/mdparser

Parsers for Molecular Dynamics related file types

gromacs molecular-dynamics parsing python topology

Last synced: 15 Dec 2024

https://github.com/lukaswittmann/molecular-dynamics-sim

Molecular dynamics simulator I programmed in order to understand MD in more detail. Periodic boundary conditions, energy minimizer, thermostat and barostat, aswell as a correct physical scale and forcefields for the noble gasses are already implemented and working well. Future steps will include parallelization of the calculation of particle interactions and maybe introducing electrostatics and complex molecules like water.

chemistry molecular-dynamics molecular-dynamics-simulation simulation

Last synced: 06 Nov 2024

https://github.com/ricalessandri/evaporate

Generate soft matter blends via simulated solvent evaporation

evaporation molecular-dynamics soft-matter-blends

Last synced: 19 Nov 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: 01 Dec 2024

https://github.com/dnlbauer/xdrfile

Rust Wrapper around the GROMACS libxdrfile library. A low level api to read and write .xtc and .trr files.

gromacs molecular-dynamics trajectories trr xdrfile xtc

Last synced: 15 Oct 2024

https://github.com/somajitdey/progrep

progrep is a command-line tool (Linux) to show live progress report, status and stats of a running simulation or compute job that executes a given number of iterations. It shows % completed, time remaining(ETA), time elapsed (both wall-clock & CPU time), number of threads, MPI_Rank(if any), CPU usage & speed (FPS). The FPS measures may be used in benchmarking, for example, while optimizing HPC algorithms for performance. progrep supports both serial (single-core/single-threaded) and parallel (multicore and/or multinode - e.g. OpenMP and/or MPI) jobs. progrep can also report for jobs running on remote hosts [Case in point: jobs running on Linux Clusters]. progrep works in client-server model. The server for progrep can be installed in your simulation source code with only 4 extra lines (API). When the progrep command is invoked, it queries this server as a client. progrep does not interfere with or slow down your simulation when not invoked. Even when invoked, the overhead is insignificant. Out of the box, the progrep API works with code written in Fortran, C and C++. If your code uses other language, please write your own wrapper for the API. The API library is small and static which benefits portability of your progrep-aware binary.

molecular-dynamics simulations

Last synced: 14 Dec 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: 23 Dec 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: 04 Dec 2024

https://github.com/simongravelle/simongravelle

README file for Github profile

github inkscape molecular-dynamics

Last synced: 08 Nov 2024

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: 19 Dec 2024

https://github.com/abelcarreras/gromorg

A python GROMACS interface for MD simulations of organic molecular crystals

gromacs molecular-dynamics molecular-mechanics python simulation

Last synced: 07 Nov 2024

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/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/joaorodrigues/pbc_mindist

Python code to calculate distances between periodic images in molecular dynamics simulations.

bioinformatics cython molecular-dynamics protein-structure python3 simulations

Last synced: 27 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: 30 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/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: 30 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/chazeon/lammps-docset

Offline documentation for LAMMPS

docset documentation lammps molecular-dynamics

Last synced: 29 Nov 2024

https://github.com/matsunagalab/tutorial_analyzingmddata

Google colab notebooks for typical MD trajectory analysis routines with Python

mdtraj molecular-dynamics scikit-learn tutorial

Last synced: 19 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/ricalessandri/scattering

Simulated scattering patterns

giwaxs molecular-dynamics self-organization

Last synced: 19 Nov 2024

https://github.com/mdsyn2019/research

PhD Molecular Dynamics Analysis Code - updated daily

chemistry molecular-dynamics molecular-modeling molecular-simulation

Last synced: 19 Nov 2024

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

Bokeh dashboard to visualize LAMMPS trajectory files

bokeh lammps molecular-dynamics visualization

Last synced: 08 Dec 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/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/simongravelle/bash-tutorial

Efficiently handle multiple simulations using bash

bash lammps molecular-dynamics tutorial

Last synced: 08 Nov 2024

https://github.com/d-seams/landing

A simple landing page

d-seams molecular-dynamics

Last synced: 22 Nov 2024

https://github.com/fandreuz/simulation-of-multibody-systems-exam

Repository for the exam in Simulation of Multibody Systems

fortran90 molecular-dynamics multibody-simulation

Last synced: 20 Nov 2024

https://github.com/snapex2409/komd

Small MD framework

kokkos md molecular-dynamics simulation

Last synced: 19 Nov 2024

https://github.com/matsunagalab/md_inputs

Place of learning OpenMM

molecular-dynamics openmm

Last synced: 19 Nov 2024

https://github.com/matsunagalab/differentiable

test-bed for differentiable parameter optimization of molecular systems

differentiable-programming docking molecular-dynamics

Last synced: 19 Nov 2024

https://github.com/matsunagalab/paper_mbar

Input files used in the paper on MBAR by Matsunaga et al.

molecular-dynamics multistate-bennett-acceptance-ratio

Last synced: 19 Nov 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/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/d-seams/wiki

A mkdocs wiki for d-SEAMS

d-seams html mkdocs molecular-dynamics wiki

Last synced: 22 Nov 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/jackrekirby/accord2

AcCoRD 2: A redesigned Actor-based Communication via Reaction-Diffusion simulator in C++.

biochemistry cpp matlab modelling molecular-dynamics

Last synced: 15 Dec 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/janjoswig/cs-msm

Core-set Markov-state model estimation

core-set markov-model molecular-dynamics python

Last synced: 15 Dec 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: 15 Dec 2024

https://github.com/aglowraph/gromacs-xvg-plot-script

A Python script for automating the plotting of .xvg files from GROMACS simulations, with dynamic labeling, time unit detection, and colorful visualization. This script reads, plots, and saves each .xvg file in the same directory, making data analysis more efficient.

automation computational-chemistry data-visualization gromacs matplotlib molecular-dynamics numpy python scientific-computing xvg-plotting

Last synced: 28 Nov 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/toruniina/rustymill

MD toolbox written in rust

molecular-dynamics pdb rust science

Last synced: 08 Dec 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/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: 15 Dec 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

Molecular Dynamics Awesome Lists
awesome-python-chemistry 149 best-of-atomistic-machine-learning 289 Awesome-Graph-Research-ICML2024 295 awesome-ai4molconformation-md 248
Molecular Dynamics Categories
GNN Theories 112 Interatomic Potentials (ML-IAP) 76 Representation Learning 51 Scene Graphs 41 General Tools 37 Language Models 28 Simulations 22 General Chemistry 19 Representation Engineering 19 Community resources 19 Datasets 17 Casual Discovery and Graphs 16 Molecular Dynamics 16 Generative Models 15 Universal Potentials 14 Mathematical tools 13 Visualization 13 GNN Applications 13 Reviews 12 Density functional theory (ML-DFT) 11