PLUMED-NEST

Project ID: plumID:24.006
Source: clusterFormationFreeEnergy/plumed.dat
Originally used with PLUMED version: 2.8
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=ps 
ENERGY
the units of energy
=eV  #KB=1.380649e-23 J/K 
The UNITS action with label  calculates somethingc1: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-300:3 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=1 D_0=3.5 D_MAX=4.5} 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
The COORDINATIONNUMBER action with label c1 calculates somethingmat: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
ATOMS
the atoms for which you would like to calculate the adjacency matrix (basically equivalent to GROUP)
=c1 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=1 D_0=3.5 D_MAX=4.5}
The CONTACT_MATRIX action with label mat calculates somethingdfs: 
DFSCLUSTERING
Find the connected components of the matrix using the depth first search clustering algorithm. More details
 
MATRIX
the input matrix (can use ARG instead)
=mat 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
The DFSCLUSTERING action with label dfs calculates the following quantities:
 Quantity   
 Description  
dfs.value
vector with length that is equal to the number of rows in the input matrixclust1: 
CLUSTER_PROPERTIES
Calculate properties of the distribution of some quantities that are part of a connected component More details
 
CLUSTERS
the label of the action that does the clustering
=dfs 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1 
SUM
 calculate the sum of all the quantities
 LOWMEM 
The CLUSTER_PROPERTIES action with label clust1 calculates somethingnat: 
CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest More details
 
CLUSTERS
the label of the action that does the clustering
=dfs 
CLUSTER
 which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
=1  
The CLUSTER_NATOMS action with label nat calculates somethingmt: 
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
=clust1.sum ...
 
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=0.02 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50   
 
SIGMA
the widths of the Gaussian hills
=1 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=373  
 
FILE
 a file in which the list of added hills is stored
=HILLS 
GRID_MIN
the lower bounds for the grid
=0 
GRID_MAX
the upper bounds for the grid
=500 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
...

The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potential
mt.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
mt.rct
the reweighting factor c(t)
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
=clust1.sum 
AT
the positions of the wall
=250.0 
KAPPA
the force constant for the wall
=0.1 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall 
The UPPER_WALLS action with label uwall calculates something
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=500