HPC Application Packages

This page provides a list of scientific applications available on the HPC systems at the MPCDF. Note that different HPC systems may host only a subset of the packages listed below. Additional software can be made available on request.

Software is generally made available via the environment modules system. The output of the command module avail provides an up-to-date list of available libraries and versions (see the section applications).

Specific information about the application, links to the documentation and – if applicable – licensing restrictions are provided via the command module help application_name.

Molecular dynamics and quantum chemistry packages

  • ABINIT A DFT simulation package

  • CP2K Ab-initio molecular dynamics

  • CPMD Ab-initio molecular dynamics

  • DFTB+ Quantum mechanical simulation software package

  • ESPResSo++ Multiscale Simulation Package for Soft Matter Systems

  • FHI-aims Ab-initio molecular simulations package

  • GROMACS Classical molecular dynamics

  • LAMMPS Classical molecular dynamics

  • NAMD Classical molecular dynamics

  • NECI Full Configuration Interaction Quantum Monte Carlo code (FCIQMC)

  • OCTOPUS Software package for performing ab-initio, time-dependent electronic structure calculations within the framework of (TD)DFT

  • ORCA Ab-initio, DFT and semiempirical SCF-MO package (for licensing reasons a valid EULA has to be presented to the MPCDF)

  • PLUMED Library for free energy calculations in molecular systems

  • Quantum Espresso A DFT simulation package

  • TURBOMOLE Program package for ab-initio electronic structure calculations (operated under a license agreement for the MPG)

  • VASP The Vienna Ab initio Simulation Package (VASP) for atomic scale materials modelling (access is restricted to VASP licensees, contact MPCDF helpdesk in order to bring in a license)

Other packages

  • AlphaFold2 Neural-network-based model to predict the three-dimensional structure of a protein based solely on its amino acid sequence. Databases and the software are readily available on Raven, cf. module help alphafold for details. Please do not install and run AlphaFold2 on the Cobra HPC system for performance reasons.

  • BioEM GPU-accelerated computing for Bayesian inference of electron microscopy images.

  • COMSOL multiphysics package (operated under a license agreement for the MPG)

  • PRESTO Software for pulsar search and analysis

  • RELION Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)