PLUMED-NEST

Project ID: plumID:19.073
Source: Paper2_setup/plumed_aa.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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
DISTANCES
Calculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=1-3,61-63  
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=82,98,114,22,38,54 
LOWEST
this flag allows you to recover the lowest of these variables
 
LOWMEM
 lower the memory requirements
The DISTANCES action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.lowest
the lowest of the quantities calculated by this action
DISTANCES
Calculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d2 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=1-3        
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=61-63              
LOWEST
this flag allows you to recover the lowest of these variables
 
LOWMEM
 lower the memory requirements
The DISTANCES action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.lowest
the lowest of the quantities calculated by this action
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cv1 
SPECIESA
this keyword is used for colvars such as the coordination number
=1-3,61-63 
SPECIESB
this keyword is used for colvars such as the coordination number
=23,24,39,40,55,56,83,84,99,100,115,116 
R_0
The r_0 parameter of the switching function
=0.25 
MORE_THAN
calculate the number of variables more than a certain target value
={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}
The COORDINATIONNUMBER action with label cv1 calculates the following quantities:
 Quantity   
 Description  
cv1.morethan
the number of values more than a target value
ENERGY
Calculate the total potential energy 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
=ene

The ENERGY action with label ene calculates a scalar quantity
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1.lowest 
AT
the positions of the wall
=0.35 
KAPPA
the force constant for the wall
=150 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
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 the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potential
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1.lowest 
AT
the positions of the wall
=0.15 
KAPPA
the force constant for the wall
=150 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall

The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potential
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
=cv1.morethan,ene 
SIGMA
the widths of the Gaussian hills
=0.01,200 
HEIGHT
the heights of the Gaussian hills
=2.5 
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 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=100 
FILE
 a file in which the list of added hills is stored
=hills_aa
GRID_MIN
the lower bounds for the grid
=-0.5,-200000 
GRID_MAX
the upper bounds for the grid
=6,-120000 
GRID_BIN
the number of bins for the grid
=526,350 
GRID_SPARSE
 use a sparse grid to store hills
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
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_aa.dat

ENDPLUMED
Terminate plumed input. More details