GMPavanLab

Swarm-CG

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

SwarmCGM

Optimization tool for calibrating coarse-grained force fields of lipids, relying on the simultaneous usage of reference AA trajectories (bottom-up) and experimental data (top-down)

cpctools

System analysis with soap fingerprints

LENS

Supporting data of submitted paper "Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling".

dynsight

A framework for the analysis of the dynamics of particle trajectories

CyclicPeptideNTs

Supporting data and molecular dynamics input data for the paper: "Self-assembly Mechanism of Cyclic Peptide Monolayers by a Supramolecular Hinge ".

DisNuc

dynNP

Repository for the code used to reproduce the analysis and the simulations for the paper "Machine Learning of Atomic Dynamics and Statistical Surface Identities in Gold Nanoparticles"

TimeSOAP

AuNP

CageReact

CGExplore

A general tool set for working with coarse-grained stk models

DefectsTracker_METALS

Descriptors

It contains all the code used for: "A data-driven approach to classify descriptors based on their efficiency in translating noisy trajectories into physically-relevant information"

DynMetSurf

Repo containing the files for "Innate Dynamics and Identity Crisis of a Metal Surface Unveiled by Machine Learning of Atomic Environments"

LEAP

MicellesML

NPsuperlattices

StrDynRel

Supporting data of submitted paper "Machine learning of microscopic structure-dynamics relationships in complex molecular systems".

Wateropti

Supporting data for wateropti paper

Azo_Peptides

This repository contains the set of data shown in the paper "Emergence of Photomodulated Protometabolism by Short Peptide-based Assemblies"

C14-Catenane

Input files for the paper "Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition". The folder contains the input files for reproducing the figure 4 of the main paper and supplementary information (mdp, topologies, plumed files, residence times, ...)

HiddenInformation

Contains all the data used in the paper "Relevant, hidden, and frustrated information in high-dimensional analyses of complex dynamical systems with internal noise"

Macrocycles2

Macrocycles3

MIMs

MultiSPbind

Optimal-Spatiotemporal-Resolutions

It contains all the code used for: "Optimal Spatiotemporal Resolutions"

Porphyrin-SPcapping

Structures and topologies of submitted paper "Controlling the length of porphyrin-based supramolecular polymers via coupled equilibria and dilution induced self-assembly"

timeseries_analysis

Code for unsupervised clustering of time-correlated data.