Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

Coarse-graining of large single-cell RNA-seq data into metacells

[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks

Martini 3 small molecule database

The source of the votca-csg and xtp packages

Sphere-Tree Construction Toolkit (unofficial repository)

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

Python data analysis package for active and soft matter simulations

A package for deriving coarse-grain potentials using MultiState Iterative Boltzmann Inversion (MS-IBI)

Tools for coarse-grained molecular dynamics simulations using the SPICA force field

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)

Collaborative repository to analyse various coarse-graining methods for networks.

A C++ implementation of the Smith - Waterman algorithm. The system consists of 3 different implementations: the one is sequential, while the other two parallelize the execution in a coarse and a fine level respectively, with the use of multithreading.

SIRAH Force Field

A toolkit for working with coarse-grain systems

MicMec, the first implementation of the micromechanical model, ever.

Coarse-grained model of titrating peptides interacting with lipid bilayers

Code for the paper "Conditional Normalizing Flows for Active Learning of Coarse-Grained Molecular Representations" (ICML 2024)

Mapping small-molecules to Martini 3 coarse-grained representations

Trajectory matching and Bayesian parametrisation to construct coarse-grained force field for polymer systems

Python scripts for the application of dissipation-corrected targeted molecular dynamics analysis.

a repo for describing how different selections of degrees of freedom affect the amount of information retained about the full system

Code for solving modified Gaussian renormalized fluctutation theory for a system of two charged plates

This repository contains the post-processed data and MATLAB scripts used to reproduce all figures presented in the manuscript and Supplementary Information (SI) of: "Nonequilibrium Self-Assembly Control by the Stochastic Landscape Method". Authors: Michael Faran and Prof. Gili Bisker.

✅ CLOSED: FTL No-Go Theorem - Rigorous proof that faster-than-light travel is fundamentally impossible in GR+QFT. Natário: 76.9% ANEC violation. QI: 10²³× gap. All warp metrics exhausted. Definitive computational reference.

Code for solving modified Gaussian renormalized fluctuation theory for a single charged surface

Analysis from the point of view of network science of the connectome of the drosophila

This is a tool to generate GROMACS input files using the SAFT-gamma Mie forcefield. The input files contain all information except the angle and torsion potentials, so add accordingly.

Graph Neural Network for Coarse-Grained Molecular Dynamics Force Fields.

Code for analysing coarse grain interaction in Protein-SSDna complexes.