Software for automated analysis of molecular dynamics trajectories

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

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

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

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

Gromacs Analysis Library for Rust

Calculate lipid order parameters from Gromacs simulations

Molecular Dynamics Trajectory Analysis Tools

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

Library for Reading Gromacs TPR Files

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

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

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

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

Repository for my senior design project/thesis code

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

"Atomic democracy" for site analysis of surfaces and bulks with known lattice structure(s).