Department of

Computational Biological Chemistry



The department is equipped with PC based workstations with high end graphic cards and dual monitors for each staff member. We have available two small compute clusters (ca. 64 cores on each of them) and >200 TB storage on highly redundant RAID systems. One of the clusters was just re-built/modernized, and is equipped with NVIDIA GPUs. In addition, we have several dedicated compute machines for specific tasks, such as machines with 16 physical cores and large amount of memory that are particularly suited for quantum chemistry calculations.

Although these facilities are complemented by external resources such as the Vienna Scientific Cluster (VSC), the department's facilities are essential. All simulation data generated in-house or on external machines are stored and analysed at our local clusters.


The software developed in our institute can be downloaded from free of charge.

Force field optimization

To facilitate force field parametrization, we have delevoped the following tools:
  • Excel-sheet to predict densities and refractive indices of ionic liquids: EXCEL-Sheet
  • Optimizing intramolecular potentials to reproduce IR spectraFFGenOpt
  • A force field conversion tool ForConX

Proton transfer reactions

During the molecular dynamics simulations in CHARMM and OpenMM, one may include proton transfer reactions:

Analysis of the trajectories

We also added some useful routines to MDAnalysis, which analyzes the MD trajectories:

Free energy calculations

Solvation and binding free energies can be computed using
Imprint: (as stipulated by Austrian law, MedienG 2005): S. Boresch / C. Schröder,
Institut für Computergestützte Biologische Chemie, Währinger Strasse 17, 1090 Wien, Austria