PLUMED-NEST

Project ID: plumID:22.025
Source: p0.026/t0.8580-recross/plumed2.inp
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

UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units

The UNITS action with label  calculates something
VOLUME
Calculate the volume of the simulation box. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=vol 
FUNC
the function you wish to evaluate
=x/17576 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=molvolThe CUSTOM action with label molvol calculates the following quantities:
 Quantity   
 Type   
 Description  
molvol
scalar
an arbitrary function

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
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=coordThe COORDINATIONNUMBER action with label coord calculates the following quantities:
 Quantity   
 Type   
 Description  
coord
vector
the coordination numbers of the specified atoms
coord_lessthan
scalar
the number of colvars that have a value less than a threshold
  
SPECIES
this keyword is used for colvars such as coordination number
=1-17576
  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=1.6 D_MAX=2.5}
  
LESS_THAN
calculate the number of variables that are less than a certain target value
={RATIONAL R_0=5 D_MAX=7.5 NN=12}
  
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER
# PLUMED interprets the command:
# COORDINATIONNUMBER ...
#   LABEL=coord
#   SPECIES=1-17576
#   SWITCH={RATIONAL R_0=1.6 D_MAX=2.5}
#   LESS_THAN={RATIONAL R_0=5 D_MAX=7.5 NN=12}
#   LOWMEM
# ... COORDINATIONNUMBER
# as follows (Click the red comment above to revert to the short version of the input):
coord_grpThe GROUP action with label coord_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_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
=1-17576
coord_matThe CONTACT_MATRIX action with label coord_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_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
=1-17576 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=1.6 D_MAX=2.5}
coord_onesThe CONSTANT action with label coord_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_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
=17576
coordThe MATRIX_VECTOR_PRODUCT action with label coord calculates the following quantities:
 Quantity   
 Type   
 Description  
coord
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 label for the matrix and the vector/scalar that are being multiplied
=coord_mat,coord_ones
coord_caverageThe MEAN action with label coord_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_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 values input to this function
=coord 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
coord_ltThe LESS_THAN action with label coord_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_lt
vector
the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: 
LESS_THAN
Use a switching function to determine how many of the input variables are less than a certain cutoff. More details
 
ARG
the values input to this function
=coord 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=5 D_MAX=7.5 NN=12}
coord_lessthanThe SUM action with label coord_lessthan calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_lessthan
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the values input to this function
=coord_lt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- End of included input --- 
COMMITTOR
Does a committor analysis. More details
 ...
  
ARG
the labels of the values which is being used to define the committor surface
=coord.lessthan
  
STRIDE
 the frequency with which the CVs are analyzed
=1
  
BASIN_LL1
List of lower limits for basin #
=0
  
BASIN_UL1
List of upper limits for basin #
=335
  
BASIN_LL2
List of lower limits for basin #
=335
  
BASIN_UL2
List of upper limits for basin #
=17576
  
NOSTOP
 if true do not stop the simulation when reaching a basin but just keep track of it
  
FILE
the name of the file on which to output the reached basin
=commit
... COMMITTOR

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=2000
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=molvol,coord.lessthan 
STRIDE
 the frequency with which the quantities of interest should be output
=200 
FILE
the name of the file on which to output these quantities
=colvar