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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/peppone98/mpro_h164n

Project of the Computational Biophysics exam @Unitn. We simulated the SARS-CoV-2 main protease Mpro with the H164N mutation in complex with two CG-376 ligands

biophysics gromacs molecular-dynamics python sars-cov-2

Last synced: 28 Dec 2024

https://github.com/adam-maz/toolkit-for-namd

I present tools that accelerate molecular dynamics (MD) simulations using NAMD software and support the analysis of the obtained trajectories.

bash clusterization gpu-acceleration medicinal-chemistry molecular-dynamics namd python

Last synced: 22 Jan 2025

https://github.com/peppone98/quantum_md_h2

The repository contains a C++ code for the quantum molecular dynamics of the hydrogen molecule. The code can be found in the folder CODE, while a discussion of the outputs and the algorithms employed can be found in the REPORT folder.

ab-initio computational-physics conjugate-gradient density-functional-theory hartree-fock molecular-dynamics quantum-mechanics quantum-physics

Last synced: 28 Dec 2024

https://github.com/peppone98/simulations_recoverin

Standard molecular dynamics and metadynamics simulations of the Recoverin protein.

free-energy-calculations funnel-meta metadynamics molecular-dynamics

Last synced: 28 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: 26 Jan 2025

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: 08 Jan 2025

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 Jan 2025

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: 01 Jan 2025

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: 08 Feb 2025

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

Generate good-looking images and movies with VMD

guide lammps molecular-dynamics tutorials vmd

Last synced: 01 Jan 2025

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 Jan 2025

Molecular Dynamics Awesome Lists
awesome-python-chemistry 149 best-of-atomistic-machine-learning 293 Awesome-Graph-Research-ICML2024 295 awesome-ai4molconformation-md 263
Molecular Dynamics Categories
GNN Theories 112 Interatomic Potentials (ML-IAP) 78 Representation Learning 52 Scene Graphs 41 General Tools 38 Language Models 28 Simulations 22 Reviews 22 General Chemistry 19 Representation Engineering 19 Community resources 19 Datasets 17 Molecular Dynamics 16 Casual Discovery and Graphs 16 Generative Models 15 Universal Potentials 13 Mathematical tools 13 GNN Applications 13 Visualization 11 Density functional theory (ML-DFT) 11