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 how to convert from the plumed default unit into that new unit or by using the shortcuts described below. This directive MUST appear at the BEGINNING of the plumed.dat file. The same units must be used througout 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.

Options

NATURAL	( default=off ) use natural units
LENGTH	the units of lengths. Either specify a conversion factor from the default, nm, or A (for angstroms) or um
ENERGY	the units of energy. Either specify a conversion factor from the default, kj/mol, or use j/mol or kcal/mol
TIME	the units of time. Either specify a conversion factor from the default, ps, or use ns or fs
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 nm - 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, irrespectively of which units you are using the 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