Starred repositories
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.
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.
To calculate membrane thickness and membrane scd parameter
Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD.
Simple drawings using vector graphics; Cairo "for tourists!"
https://github.com/felixonmars/BaiduPCS-Go/releases
jintuzhang / mlcolvar
Forked from luigibonati/mlcolvarA unified framework for machine learning collective variables for enhanced sampling simulations
aimmd (AI for Molecular Mechanism Discovery) autonomously steers (a large number of) molecular dynamics simulations to efficiently sample and understand rare transition events.
Some collected tools for molecular simulation pipelines
Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM