Software

PyDiffusion

Description: PyDiffusion is a python library to analyze the rotational and translational diffusion of molecules in molecular dynamics simulation or rigid body simulations.
Developers: Max Linke, Gerhard Hummer

CNT-GAFF

Description: Builds atomistic structures of carbon nanotubes with the possibility to add functional groups (OH, COOH, COO-) and assigns generalized Amber (GAFF) parameters to them.
Developers: Martin Vögele

CAPRIQORN

CAlculation of P(R) and I(Q) Of macRomolecules in solutioN Description: Calculation SAXS/WAXS scattering intensities and pair-distance distribution functions directly from the output trajectories of molecular dynamics simulations using explicit solvent.
Developers: Jürgen Köfinger, Klaus Reuter, and contributers.

CADISHI

CAlculation of DIStance HIstograms Description: Fast computations of histograms of the (Euclidean) distances between objects.
Developers: Klaus Reuter and Jürgen Köfinger

PyDHAMed

Description: Dynamic Histogram Analysis extended to detailed balance
Developers: Lukas S. Stelzl, Gerhard Hummer, and contributors.

MDBenchmark

Description: Benchmark and scaling studies for MD simulations
Developers: Max Linke, Michael Gecht, and contributors.

BioEM

Bayesian Inference Of Electron Microscopy Description: The method enables the characterisation of structural models by calculating their posterior probability with respect to individual electron microscopy images.

Software of the Department of Theoretical Biophysics