Introducing OMMProtocol

A command line application to launch molecular dynamics simulations with OpenMM

  • No coding required - just a YAML input file!
  • Smart support for different input file formats:
    • Topology: PDB/PDBx, Mol2, Amber’s PRMTOP, Charmm’s PSF, Gromacs’ TOP, Desmond’s DMS
    • Positions: PDB, COOR, INPCRD, CRD, GRO, DCD
    • Velocities: PDB, VEL
    • Box vectors: XSC, CSV, PDB, GRO, INPCRD, DCD
    • A fallback method is implemented and will attempt to load everything else that might be supported by ParmEd.
  • Choose your preferred trajectory format (PDB, PDBx, DCD, HDF5, NETCDF, MDCRD) and checkpoints (Amber’s, CHARMM’s, OpenMM XML states).
  • Live report of simulation progress, with estimated ETA and speed.
  • Checkpoint every n steps. Also, emergency rescue files are created if an error occurs.
  • Autochunk the trajectories for easy handling.

For developers