PLUMED-NEST

Project ID: plumID:19.054
Source: plumed.dat
Originally used with PLUMED version: 2.3
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
=0.001  #Amstroeng, hartree, fs

The UNITS action with label  calculates somethingeneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the value calculated by this action: 
ENERGY
Calculate the total potential energy of the simulation box. More details
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,2 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
d5The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,6 
NOPBC
 ignore the periodic boundary conditions when calculating distances

c1The COMBINE action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
a linear compbination:  
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1,d5 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.500,-0.500 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

h1The DISTANCE action with label h1 calculates the following quantities:
 Quantity   
 Type   
 Description  
h1
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,3 
NOPBC
 ignore the periodic boundary conditions when calculating distances
h2The DISTANCE action with label h2 calculates the following quantities:
 Quantity   
 Type   
 Description  
h2
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,4 
NOPBC
 ignore the periodic boundary conditions when calculating distances
h3The DISTANCE action with label h3 calculates the following quantities:
 Quantity   
 Type   
 Description  
h3
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,5 
NOPBC
 ignore the periodic boundary conditions when calculating distances

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
=+4.0 
KAPPA
the force constant for the wall
=150.0 
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_1The UPPER_WALLS action with label uwall_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_1.bias
scalar
the instantaneous value of the bias potential
uwall_1.force2
scalar
the instantaneous value of the squared force due to this bias potential
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
=+4.0 
KAPPA
the force constant for the wall
=150.0 
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_2The UPPER_WALLS action with label uwall_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_2.bias
scalar
the instantaneous value of the bias potential
uwall_2.force2
scalar
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 arguments on which the bias is acting
=h1 
AT
the positions of the wall
=+1.7 
KAPPA
the force constant for the wall
=150.0 
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
=lwall_1The LOWER_WALLS action with label lwall_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall_1.bias
scalar
the instantaneous value of the bias potential
lwall_1.force2
scalar
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 arguments on which the bias is acting
=h2 
AT
the positions of the wall
=+1.7 
KAPPA
the force constant for the wall
=150.0 
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
=lwall_2The LOWER_WALLS action with label lwall_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall_2.bias
scalar
the instantaneous value of the bias potential
lwall_2.force2
scalar
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 arguments on which the bias is acting
=h3 
AT
the positions of the wall
=+1.7 
KAPPA
the force constant for the wall
=150.0 
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
=lwall_3The LOWER_WALLS action with label lwall_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall_3.bias
scalar
the instantaneous value of the bias potential
lwall_3.force2
scalar
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
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
 
ARG
the input for this action is the scalar output from one or more other actions
=c1
 
PACE
the frequency for hill addition
=50
 
HEIGHT
the heights of the Gaussian hills
=2.0
 
SIGMA
the widths of the Gaussian hills
=0.1
 
FILE
 a file in which the list of added hills is stored
=HILLS
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 
GRID_MIN
the lower bounds for the grid
=-4
 
GRID_MAX
the upper bounds for the grid
=+4
 
GRID_BIN
the number of bins for the grid
=1000
... METAD


PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d5,c1,metad.*,ene
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
=1