marrink-lab

polyply_1.0

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

vermouth-martinize

Describe and apply transformation on molecular structures and topologies

TS2CG

TS2CG: Conversion of triangulated surfaces to (coarse grain) membrane models for molecular simulation

MDVoxelSegmentation

A voxel based approach for dynamic cluster analysis of molecular dynamics trajectories.

martini-forcefields

Collection of interaction and molecule parameters for the Martini3 force-field

cartographer

gromit

Auxiliary tools for automated atomistic and coarse-grained molecular dynamics simulations using gromacs

Martini_Minimal_Cell

martini-workshop

Martini Workshop: Simulating a Minimal Bacterial Cell

Martini3-small-molecules

Martini 3 small-molecule database

shocker

Setting up and running simulations imitating the process of osmotic shocking

TS2CG1.1

TS2CG version 1.1

bentopy

Packs stuff in boxes

PEGylated_proteins_tutorial

Files required for our tutorial on PEGylated proteins

martini_sour

Setup and run titratable Martini simulations

martini_sour_examples

Examples corresponding to marrink-lab/martini_sour

martinize-examples

Examples for Martinize2 and vermouth

polyply_regression_tests

Regression tests and tutorial input files for the polyply software suite

pycgbuilder

A Qt5 based GUI for making mapping files

VisualizationServer

Managing all issues and suggestions regarding the Visualization Server. This tracking is meant for issues raised by users both inside the Molecular Dynamics group, and users within the University of Groningen.

cgbuilder

Build coarse-grained mapping for molecules from a web-GUI