PLUMED-NEST

Project ID: plumID:19.071
Source: MFI_paper_scripts/2D_double_well/plumed.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

pThe DISTANCE action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.x
scalar
the x-component of the vector connecting the two atoms
p.y
scalar
the y-component of the vector connecting the two atoms
p.z
scalar
the z-component of the vector connecting the two atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,2 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
ffThe MATHEVAL action with label ff calculates the following quantities:
 Quantity   
 Type   
 Description  
ff
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(-3*x^2+x^4-3*x*y+y^4
bbThe BIASVALUE action with label bb calculates the following quantities:
 Quantity   
 Type   
 Description  
bb.bias
scalar
the instantaneous value of the bias potential
bb.ff_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named ff: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ff

METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y 
SIGMA
the widths of the Gaussian hills
=0.1,0.1 
HEIGHT
the heights of the Gaussian hills
=0.05 
PACE
the frequency for hill addition
=500 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential 
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y 
SIGMA
the widths of the Gaussian hills
=0.1,0.1 
HEIGHT
the heights of the Gaussian hills
=0.05 
PACE
the frequency for hill addition
=500 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad  
FILE
 a file in which the list of added hills is stored
=HILLS


PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=position 
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y