COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
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Updated
May 13, 2024 - Python
COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
A toolkit for working with coarse-grain systems
Generate and perturb protein structural ensembles using the ExProSE algorithm
Massively parallel hybrid particle-field molecular dynamics in Python.
⚡ general purpose coarse-grained molecular dynamics simulation package
Analyze two-component nanoparticle properties for classical molecular dynamics simulations
This repo consists of Monte Carlo C++ codes used to run coarse-grained simulations for biopolymers like DNA.
Files required for our tutorial on PEGylated proteins
Molecular Dynamics Trajectory Analysis Tools
Object-Oriented Perl 5, Moose Library for Molecular Hacking
Differentiable molecular simulation of proteins with a coarse-grained potential
Massively parallel hybrid particle-field molecular dynamics (hPF-MD) simulation method in Julia
Tutorial examples for HylleraasMD
Simulating tumour development in two and three dimensions using the framework of the spatial Tangled Nature model
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
Force field parameters and supplementary scripts for the "A coarse-grained model for DNA origami" paper by R. Reshetnikov, A. Stolyarova, A. Zalevsky et. al.
Molecular simulator for proteins that uses Go-type potentials
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