coarse-graining
There are 0 repository under coarse-graining topic.
- polyply_1.0
marrink-lab / polyply_1.0
Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
Language:Python 109 kyonofx / mlcgmd
[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks
Language:Python 60GfellerLab / SuperCell
Coarse-graining of large single-cell RNA-seq data into metacells
Language:R 55ricalessandri / Martini3-small-molecules
Martini 3 small-molecule database
Language:Shell 49- Language:C++ 43
- Swarm-CG
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
Language:Python 37 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)
Language:Python 8gabriele-di-bona / CoarseNet
Collaborative repository to analyse various coarse-graining methods for networks.
Language:Jupyter Notebook 7SPICA-group / spica-tools
Tools for coarse-grained molecular dynamics simulations using the SPICA force field
Language:Python 7- Language:Python 6
- smith-waterman-algorithm
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.
Language:C++ 4 Martini 3 small-molecule database
Language:Shell 4Mapping small-molecules to Martini 3 coarse-grained representations
SIRAHFF / documentation
SIRAH Force Field
- Language:Python 3
- amep
amepproject / amep
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
Language:Python 2 gitesei / SI-peptidebilayer
Coarse-grained model of titrating peptides interacting with lipid bilayers
Language:Jupyter Notebook 2markjenei94 / polymerisation-coarse-graining
Trajectory matching and Bayesian parametrisation to construct coarse-grained force field for polymer systems
Language:Jupyter Notebook 2floWneffetS / dcTMD_scripts_v1.0
Python scripts for the application of dissipation-corrected targeted molecular dynamics analysis.
Language:Python 1mazfayaz / gromacsSaftGen
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.
Language:Python 1mballarin97 / DrosophilaNetwork
Analysis from the point of view of network science of the connectome of the drosophila
Language:Jupyter Notebook 1mgiulini / pymap
a repo for describing how different selections of degrees of freedom affect the amount of information retained about the full system
Language:Python 1M4Marvin / Dissertation-MS
Code for analysing coarse grain interaction in Protein-SSDna complexes.
Language:HTML 0nikhil0165 / one_plate_mgrf
Code for solving modified Gaussian renormalized fluctuation theory for a single charged surface
Language:Python 0Code for solving modified Gaussian renormalized fluctutation theory for a system of two charged plates
Language:Python 0ppieczywek / molecules-clustering-algorithm
Algorithm designed to aggregate non-bounded MD (water) molecules in order to map their parameters into the coarse-grained model.
Language:MATLAB 0RSMI-NE / ABsuperdimers
Constructing coarse grained super-dimers on the Ammann-Beenker quasicrystal with RSMI-NE.
Language:Jupyter Notebook 0ktaletsk / CPF
Jupyter Notebooks for coarse-graining physical models using Constant Probability Flux (CPF) method
Language:Jupyter NotebookPeppone98 / Multiscale_Recoverin
A coarse-grained analysis of the Recoverin protein for the exam of Multiscale Methods
Language:Jupyter Notebook
