FlexMD functionality summary
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**Molecule**

Input/output

* Reads and writes PDB and XYZ files

* Reads and writes topology data (in CHARMM format)

* Reads and writes force field data (in CHARMM format)

Analysis

* 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 a periodic box

Water specific

* Finds hydrogen bonds

* Finds the shortest water bridge connecting H-donor and acceptor

**Energy and force calculations**

Standard

* ADF

* DFTB

* REAXFF

* UFF

* MOPAC

* NAMD

* Lennard-Jones force fields

Multi-scale

* 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
