UNITS
This is part of the setup module

This command sets the internal units for the code.

A new unit can be set by either specifying a conversion factor from the plumed default unit or by using a string corresponding to one of the defined units given below. This directive MUST appear at the BEGINNING of the plumed.dat file. The same units must be used throughout the plumed.dat file.

Notice that all input/output will then be made using the specified units. That is: all the input parameters, all the output files, etc. The only exceptions are file formats for which there is a specific convention concerning the units. For example, trajectories written in .gro format (with DUMPATOMS) are going to be always in nm.

The following strings can be used to specify units. Note that the strings are case sensitive.

  • LENGTH: nm (default), A (for Angstrom), um (for micrometer), Bohr (0.052917721067 nm)
  • ENERGY: kj/mol (default), j/mol, kcal/mol (4.184 kj/mol), eV (96.48530749925792 kj/mol), Ha (for Hartree, 2625.499638 kj/mol)
  • TIME: ps (default), fs, ns, atomic (2.418884326509e-5 ps)
  • MASS: amu (default)
  • CHARGE: e (default)
Options
NATURAL

( default=off ) use natural units

LENGTH the units of lengths. Either specify a conversion factor from the default, nm, or use one of the defined units, A (for angstroms), um (for micrometer), and Bohr.
ENERGY the units of energy. Either specify a conversion factor from the default, kj/mol, or use one of the defined units, j/mol, kcal/mol and Ha (for Hartree)
TIME the units of time. Either specify a conversion factor from the default, ps, or use one of the defined units, ns, fs, and atomic
MASS the units of masses. Specify a conversion factor from the default, amu
CHARGE the units of charges. Specify a conversion factor from the default, e
Examples
# this is using Angstrom - kj/mol - fs
UNITS LENGTH=A TIME=fs

# compute distance between atoms 1 and 4
d: DISTANCE ATOMS=1,4

# print time and distance on a COLVAR file
PRINT ARG=d FILE=COLVAR

# dump atoms 1 to 100 on a 'out.gro' file
DUMPATOMS FILE=out.gro STRIDE=10 ATOMS=1-100

# dump atoms 1 to 100 on a 'out.xyz' file
DUMPATOMS FILE=out.xyz STRIDE=10 ATOMS=1-100

In the COLVAR file, time and distance will appear in fs and A respectively, irrespective of which units you are using in the host MD code. The coordinates in the out.gro file will be expressed in nm, since gro files are by convention written in nm. The coordinates in the out.xyz file will be written in Angstrom since we used the UNITS command setting Angstrom units. Indeed, within PLUMED xyz files are using internal PLUMED units and not necessarily Angstrom!

If a number, x, is found instead of a string, the new unit is equal to x times the default units. Using the following command as first line of the previous example would have lead to an identical result: 

UNITS LENGTH=0.1 TIME=0.001