FlexMD functionality summaryΒΆ



  • Reads and writes PDB and XYZ files

  • Reads and writes topology data (in CHARMM format)

  • Reads and writes force field data (on CHARMM format)


  • Extracts geometry data

Drawing functionality

  • Adds atoms and bonds

  • Changes bond-lengths, angles and torsions

  • Cuts fragments

  • Cuts solvent boxes and droplets

  • Performs rotations and translations, to fit bonds to axes and planes

Periodic functionality

  • Adds periodic images

  • Wraps molecules into periodic box

Water specific

  • Finds hydrogen bonds

  • Finds shortest water bridge connecting H-donor and acceptor

Energy and force calculations


  • ADF

  • DFTB


  • UFF


  • NAMD

  • Lennard-Jones force fields


  • QM/MM, mechanical embedding: Combines all the codes above

  • Hybrid: More flexible than QM/MM. Combines different force calculations by summing or subtracting the energies and forces. The standard calculations (above) can therefore be combined with:

    • Metadynamics

    • Plumed (external code that computes free energy data)

    • Constraints

  • Adaptive QM/MM (for chemistry in solution)

    • Difference-based Adaptive Solvation (DAS)

    • Sorted Adaptive Partitioning (SAP)

    • Buffered-Core (BC)

    • Flexible Inner Region Ensemble Separator (FIRES)

Molecular Dynamics

  • Uses ASE as the molecular dynamics driver for all above methods

  • Analyses trajectories