Tsjerk

Insane

INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems

MartiniTools

Backward

Mapping from Coarse Grain Models to Atomistic (and Back)

Martinize

Martini Molecular Dynamics Tools

xtc

Light-weight processing of Gromacs' XTC trajectories

simopt

SIMple OPTion parser

gromacs

Public/backup repository of the gromacs molecular simulation toolkit

gromit

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

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

pdbsearch

Python powered search facilities for the RCSB protein databank

vesicle

datasets

A collection of datasets used in education

GitPresentation

Presentation material for MD lab git tutorial

martinize.py

Create coarse grain Martini input files for Gromacs from (atomistic) pdb files.

MDVoxelClustering

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

pdbquery

Python API and command line tool for querying the Protein DataBank

pmda

Parallel algorithms for MDAnalysis

pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

progbio

Teaching materials for classes teaching programming to biologists

pymeca

Python Molecular Ensemble Component Analysis

STA5

Bioinformatics@Hanze-UAS Statistics Module 5

taw

Trajectory Analysis Workbench

Tipsi

Transition/Interface Path Sampler Identifier - A Gromacs-based TPS/TIS companion.

vakomschrijvingen_bioinformatica

Xelsea

*xelsea is a package for efficient analysis of coordinate data through binning in cells with alternative shapes: rectangular (pixels, voxels), hexagonal (hixels), rhombic dodecahedral (doxels) or triclinic (trixels), all with support for periodic boundary conditions.