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

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

Martini 3 small-molecule database

The source of the votca-csg and xtp packages

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

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)

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

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

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

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

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

Mapping small-molecules to Martini 3 coarse-grained representations

Martini 3 small-molecule database

A toolkit for working with coarse-grain systems

Coarse-grained model of titrating peptides interacting with lipid bilayers

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

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.