Domain Biomedical research domain
Description Quantum Mechanical Fragment Molecular Orbital (FMO) based Fragment Expansion. FMO based Virtual Screen.
User’s guide
Scientific articles
Computational requirements Programming language: Fortran
Dependencies: MPICH
Memory requirements: 3GB per core
Disk requirements: Small for most calculations ~150KB. However will require the access to the EvoSource Small molecule library. Is 7Million compounds in SDF format. As single conformers will be used should only require 177GB of data storage space for input. Will potentially be running 21 million calculation using the DFTB functional. Keeping all this data could lead to ~3 terabytes of data if all results are kept. Energy + Geometries could be extracted from results and other from FMO run deleted.
Complementary tools:
Type of software licence Open
Input requirements Format: Text file GAMESS.inp (including pdb and ligand)
Coming from: Generated by KNIME at evotec
Disk use: FMO Fragment Screen = 3000 input jobs containing geometries. FMO DFTB virtual screen = 21 million input jobs containing geometries
Output requirements Format: Text GAMESS.out (including pdb and ligand)
Used by: Potential post processing by cclib to extract energies / geometries. Will need to be sorted to show best docked ligands / fragments
Disk use: 3000 + ~21 million
Performance and HPC profile
Parallelism Type of parallelism: MPI sockets or Infiniband
Scalability: FMO standard = 64 cores in groups of ~16 or 80 cores in Groups of 20. FMO DFTB = 1 core but potentially Millions of Jobs
Mode of operation Standard FMO = ~64 cores in groups of ~16 or 80 cores in Groups of 20. FMO DFTB = 1 core but potentially millions of Jobs
Deployed on Frequently installed centrally on HPC resources (for example SuperMUC, Cartesius, Archer)
Getting started
Benchmarks and examples
Instructions for running on dedicated platforms