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