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

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

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

The Active Matter Evaluation Package (AMEP) - a Python library for the analysis of particle-based and continuum simulation data of soft and active matter systems

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)

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

A toolkit for working with coarse-grain systems

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

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.

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 fluctuation theory for a single charged surface

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

A package that contains tools for mapping to and modifying CG models