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)

Examples

Click on the labels of the actions for more information on what each action computes

# this is using Angstrom - kj/mol - fs
UNITS LENGTHthe units of lengths. 
=A TIMEthe units of time. 
=fs The UNITS action with label 
# compute distance between atoms 1 and 4
d: DISTANCE ATOMSthe pair of atom that we are calculating the distance between. 
=1,4 The DISTANCE action with label d calculates a single scalar value
# print time and distance on a COLVAR file
PRINT ARGthe input for this action is the scalar output from one or more other actions. 
=d FILEthe name of the file on which to output these quantities 
=COLVAR The PRINT action with label 
# dump atoms 1 to 100 on a 'out.gro' file
DUMPATOMS FILEcompulsory keyword 
file on which to output coordinates; extension is automatically detected 
=out.gro STRIDEcompulsory keyword ( default=1 )
the frequency with which the atoms should be output 
=10 ATOMSthe atom indices whose positions you would like to print out. 
=1-100 The DUMPATOMS action with label 
# dump atoms 1 to 100 on a 'out.xyz' file
DUMPATOMS FILEcompulsory keyword 
file on which to output coordinates; extension is automatically detected 
=out.xyz STRIDEcompulsory keyword ( default=1 )
the frequency with which the atoms should be output 
=10 ATOMSthe atom indices whose positions you would like to print out. 
=1-100 The DUMPATOMS action with label

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:

Click on the labels of the actions for more information on what each action computes

UNITS LENGTHthe units of lengths. 
=0.1 TIMEthe units of time. 
=0.001 The UNITS action with label

Glossary of keywords and components

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