Comments

If you are an organized sort of person who likes to remember what the hell you were trying to do when you ran a particular simulation you might find it useful to put comments in your input file. In PLUMED you can do this as comments can be added using a # sign. On any given line everything after the # sign is ignored so erm... yes add lines of comments or trailing comments to your hearts content as shown below (using Shakespeare is optional):

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

# This is the distance between two atoms:
d1: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label d1 calculates a single scalar value
Snout: UPPER_WALLS 
ARG
the input for this action is the scalar output from one or more other actions. 
=d1 
AT
compulsory keyword 
the positions of the wall. 
=3.0 
KAPPA
compulsory keyword 
the force constant for the wall. 
=3.0 # In this same interlude it doth befall. The UPPER_WALLS action with label Snout calculates the following quantities:

 Quantity   
 Description  
Snout.bias
the instantaneous value of the bias potential
Snout.force2
the instantaneous value of the squared force due to this bias potential


# That I, one Snout by name, present a wall.

(see DISTANCE and UPPER_WALLS)

An alternative to including comments in this way is to use the command ENDPLUMED. Everything in the PLUMED input after this keyword will be ignored.