PLUMED-NEST

Project ID: plumID:21.009
Source: npt-committor/smd/plumed.inp
Originally used with PLUMED version: 2.6
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

The UNITS action with label  calculates something
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_morethan
scalar
the number of colvars that have a value more than a threshold
  
SPECIES
this keyword is used for colvars such as coordination number
=1-512
  
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=5.0 D_MAX=10.0}
  
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=5.0 D_MAX=5.5}
  
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER
# PLUMED interprets the command:
# COORDINATIONNUMBER ...
#   LABEL=coord
#   SPECIES=1-512
#   SWITCH={RATIONAL R_0=5.0 D_MAX=10.0}
#   MORE_THAN={RATIONAL R_0=5.0 D_MAX=5.5}
#   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
=1-512
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
=1-512 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=5.0 D_MAX=10.0}
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
=512
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_mtThe MORE_THAN action with label coord_mt calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_mt
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: 
MORE_THAN
Use a switching function to determine how many of the input variables are more 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=5.0 D_MAX=5.5}
coord_morethanThe SUM action with label coord_morethan calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_morethan
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_mt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- End of included input --- 
MOVINGRESTRAINT
Add a time-dependent, harmonic restraint on one or more variables. More details
 ...
  
ARG
the labels of the scalars on which the bias will act
=coord.morethan
  
STEP0
This keyword appears multiple times as STEPx with x=0,1,2,
=0       
AT0
ATx is equal to the position of the restraint at time STEPx
=0.0  
KAPPA0
KAPPAx is equal to the value of the force constants at time STEPx
=10.0
  
STEP1
This keyword appears multiple times as STEPx with x=0,1,2,
=2000000 
AT1
ATx is equal to the position of the restraint at time STEPx
=19.0 
KAPPA1
KAPPAx is equal to the value of the force constants at time STEPx
=10.0
... MOVINGRESTRAINT

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
=200000
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=coord.morethan 
STRIDE
 the frequency with which the quantities of interest should be output
=2000 
FILE
the name of the file on which to output these quantities
=colvar