coarse-graining 开源项目推荐（61 个）

marrink-lab /polyply_1.0

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

GfellerLab /SuperCell

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

kyonofx /mlcgmd

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

Martini-Force-Field-Initiative /M3-Small-Molecules

Martini 3 small molecule database

votca /votca

The source of the votca-csg and xtp packages

mlund /spheretree

Sphere-Tree Construction Toolkit (unofficial repository)

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

amepproject /amep

Python data analysis package for active and soft matter simulations

mosdef-hub /msibi

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

SPICA-group /spica-tools

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

tummfm /cg-bg

[ICML 2026] Coarse-Grained Boltzmann Generators

GMPavanLab /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)

giorgapost /smith-waterman-algorithm

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.

SIRAHFF /documentation

SIRAH Force Field

gabriele-di-bona /CoarseNet

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

cmelab /grits

A toolkit for working with coarse-grain systems

molmod /micmec

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

gitesei /SI-peptidebilayer

Coarse-grained model of titrating peptides interacting with lipid bilayers

JohnsonBiophysicsLab /ionerdss

Transforming macromolecular structures to self-assembly simulations

aimat-lab /coarse-graining-AL

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