Massively parallel hybrid particle-field molecular dynamics in Python.
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Updated
Sep 6, 2024 - Python
Massively parallel hybrid particle-field molecular dynamics in Python.
COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
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
A toolkit for working with coarse-grain systems
Generate and perturb protein structural ensembles using the ExProSE algorithm
⚡ 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
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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