molecular-dynamics-analysis

C++ toolkit for post-processing molecular dynamics trajectories, with a focus on high-performance static and dynamic analyses of amorphous/glassy/polymer materials.

Structural analysis tools for OpenFE free energy calculations, built on MDAnalysis.

Building and analyzing residue interaction networks with cofactors (includes tutorial).

Calculate lipid order parameters from Gromacs simulations

Efficiently compute off-resonance Raman spectra from first principles calculations (e.g. VASP) using polynomial models and machine learning..

Gromacs Analysis Library for Rust

A Jekyll website for the research guides--UNIX, AMBER, Analysis, and R.

Machine Learning Transition State Analysis (MLTSA) suite with Analytical models to create data on demand and test the approach on different types of data and ML models.

Order parameter calculations from Desmond Maestro .csv out files

Molecular Dynamics Trajectory Analysis Tools

CONAN is a tool to generate carbon and boron nitride structures, and to analyze molecular dynamics trajectories composed of a liquid at solid interfaces.

Library for Reading Gromacs TPR Files

A Python module for performing data analysis of atomistic trajectories relevant for glasses and supercooled liquids.

A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan

A package to find collective variables of dynamical systems by training neural networks

Reactive molecular dynamics trajectory analysis

A package for multiple-scale simulations on the dynamical and kinetic processes in materials

Center Any Group in a Gromacs Trajectory

Reproducible Python pipeline for molecular docking, virtual screening, GROMACS molecular dynamics and MM-PBSA analysis.

This repository contains Jupyter notebooks used to perform computational analysis of LAT1 (SLC7A5) cholesterol binding sites, as published in JCTC