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

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

OpenMM plugin to interface with PLUMED

Coarse-Grained Smiles (CGsmiles) for representing abitrarily complex molecules using a compact line notation

The source of the votca-csg and xtp packages

Generate PEG topology for GROMACS and LAMMPS

Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations

Create beautiful slides on the web using Claude's frontend skills

This is a short tutorial on how to perform a peptide-membrane interaction simulation using the Martini force field, together with the Gromacs package.

Scripts empleados durante el desarrollo de mi tesis