Units in the Colvars module

The ``internal units'' of the Colvars module are the units in which values are expected to be in the configuration file, and in which collective variable values, energies, etc. are expressed in the output and colvars trajectory files. Generally the Colvars module uses internally the same units as its back-end MD engine, with the exception of VMD, where different unit sets are supported to allow for easy setup, visualization and analysis of Colvars simulations performed with any simulation engine.

Note that angles are expressed in degrees, and derived quantites such as force constants are based on degrees as well. Atomic coordinates read from XYZ files (and PDB files where applicable) are expected to be expressed in Ångström, no matter what unit system is in use by the back-end or the Colvars Module.

To avoid errors due to reading configuration files written in a different unit system, it can be specified within the input:

• units $\langle\,$ Unit system to be used$\,\rangle$
  Context: global
  Acceptable values: string
  Description: A string defining the units to be used internally by Colvars. Allowed values are: real (Å, kcal/mol), gromacs (nm, kJ/mol), metal (Å, eV), and electron (Bohr, Hartree). In VMD, the default system of units for Colvars is VMD's native units: real (Å, kcal/mol). However, the units keyword will switch to a different unit system than the current one if no colvars were defined before reading the current configuration. If colvars are already defined, units will refuse changing the unit system to avoid making the definition of those variables erroneous in the new system of units. If needed this precaution can be overridden using the cv units scripting command ().