A step-by-step tutorial to run Molecular Dynamics Simulations with enhanced sampling of a pepitide using PLUMED implemented in GROMACS to perform replica exchanges

The repository for storing the lessons for the PLUMED tutorials site

Implementation of PLUMED keywords for use in research projects

A collection of simulation recipes for the atomic-scale modeling of materials and molecules

Data and code for "Quasi-one-dimensional hydrogen bonding in nanoconfined ice"

Repository holding all the files required for PLUMED online tutorial.

Optimized codes for fast molecular dynamics

Flow Matching for Electron Redistribution

Collection of tutorials to use the MACE machine learning force field.

Python code for mechanistic dataset generation

Source code of 'Deep transfer operator learning for partial differential equations under conditional shift'.

Input files and results of paper: Multithermal-multibaric molecular simulations from a variational principle, Pablo Piaggi and Michele Parrinello, Phys. Rev. Lett. 122, 050601 (2019) ; https://doi.…

Computing RESP charges of ligands in the local enviroment using QMMM

SevenNet - a graph neural network interatomic potential package supporting efficient multi-GPU parallel molecular dynamics simulations.

Calculate 2D maps of membrane thickness from Gromacs simulations.

OpenMM is a toolkit for molecular simulation using high performance GPU code.

A script for reading lammps data

To calculate membrane thickness and membrane scd parameter

Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD.

Examples and tutorials of using MDAnalysis

Simple drawings using vector graphics; Cairo "for tourists!"

https://github.com/felixonmars/BaiduPCS-Go/releases

A unified framework for machine learning collective variables for enhanced sampling simulations