pyHVis3D calculates hydrogen bonds (H-bonds) resulting from molecular simulation trajectories and allows for an easy to interpret 3D visualisation.

pyHVis3D is available as standalone executable for Fedora 25 and Windows 7 as well as python source code. The software (including manual and test cases) can be downloaded here:

Download pyHVis3D

If you use this software for publications please cite:
Bernhard Knapp, Marta Alcala, Hao Zhang, Clare E. West, P. Anton van der Merwe, Charlotte M. Deane. pyHVis3D: Visualising Molecular Simulation deduced H-bond networks in 3D: Application to T-cell receptor interactions. In review. 2017.
H-bond network of two T-cell receptors visualised with pyHVis3D.

An older and deprecated version based on Gromacs, Matlab, and VMD (entitled H-Vis-3D) is available here. Use of this version is no longer recommended.