PLUMED-NEST

Project ID: plumID:22.008
Source: LJ-cluster/plumed.dat
Originally used with PLUMED version: 2.7
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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=0.0101805 
ENERGY
the units of energy
=96.4853329
The UNITS action with label  calculates something
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-7 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=comThe COM action with label com calculates the following quantities:
 Quantity   
 Type   
 Description  
com
atoms
virtual atom calculated by COM action
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d1 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d2 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d3The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3
scalar
the DISTANCE between this pair of atoms
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d3 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=4,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d4The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4
scalar
the DISTANCE between this pair of atoms
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d4 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d5The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5
scalar
the DISTANCE between this pair of atoms
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d5 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d6The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d6
scalar
the DISTANCE between this pair of atoms
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d6 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d7The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Type   
 Description  
d7
scalar
the DISTANCE between this pair of atoms
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d7 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
c1The COORDINATIONNUMBER action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
vector
the value calculated by this action: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-7 
MOMENTS
the list of moments that you would like to calculate
=2-3 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=1.5 NN=8 MM=16}
# PLUMED interprets the command:
# c1: COORDINATIONNUMBER SPECIES=1-7 MOMENTS=2-3 SWITCH={RATIONAL R_0=1.5 NN=8 MM=16}
# as follows (Click the red comment above to revert to the short version of the input):
c1_grpThe GROUP action with label c1_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_grp
atoms
indices of atoms specified in GROUP: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-7 
c1_matThe CONTACT_MATRIX action with label c1_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
GROUP
specifies the list of atoms that should be assumed indistinguishable
=1-7 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=1.5 NN=8 MM=16} 
c1_onesThe CONSTANT action with label c1_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=7
c1The MATRIX_VECTOR_PRODUCT action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the input for this action is the scalar output from one or more other actions
=c1_mat,c1_ones 
c1_caverageThe MEAN action with label c1_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_caverage
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=c1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
c1_diffpow-2The CUSTOM action with label c1_diffpow-2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_diffpow-2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=c1,c1_caverage 
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
=(x-y)^2 
c1_moment-2The MEAN action with label c1_moment-2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_moment-2
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=c1_diffpow-2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
c1_diffpow-3The CUSTOM action with label c1_diffpow-3 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_diffpow-3
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=c1,c1_caverage 
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
=(x-y)^3 
c1_moment-3The MEAN action with label c1_moment-3 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_moment-3
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the input to this function
=c1_diffpow-3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=c1 
HEIGHT
the heights of the Gaussian hills
=0.05 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.1,0.1 
GRID_MIN
the lower bounds for the grid
=-1.5,-1.5 
GRID_MAX
the upper bounds for the grid
=2.5,2.5 
GRID_BIN
the number of bins for the grid
=500,500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5 
FILE
 a file in which the list of added hills is stored
=HILLS