PLUMED-NEST

Project ID: plumID:22.008
Source: LJ-cluster/plumed.dat
Originally used with PLUMED version: 2.7
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
=0.0101805 
ENERGY
the units of energy
=96.4853329
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-7 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=com
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1
The DISTANCE action with label d1 calculates a scalar quantity
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
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d2
The DISTANCE action with label d2 calculates a scalar quantity
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
=d2 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d3
The DISTANCE action with label d3 calculates a scalar quantity
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
=d3 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=4,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d4
The DISTANCE action with label d4 calculates a scalar quantity
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
=d4 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d5
The DISTANCE action with label d5 calculates a scalar quantity
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
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d6
The DISTANCE action with label d6 calculates a scalar quantity
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
=d6 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,com 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d7
The DISTANCE action with label d7 calculates a scalar quantity
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
=d7 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=100
c1: 
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
=1-7 
MOMENTS
the list of moments that you would like to calculate
=2-3 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=1.5 NN=8 MM=16}
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
=c1 
HEIGHT
the heights of the Gaussian hills
=0.05 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.1,0.1 
GRID_MIN
the lower bounds for the grid
=-1.5,-1.5 
GRID_MAX
the upper bounds for the grid
=2.5,2.5 
GRID_BIN
the number of bins for the grid
=500,500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5 
FILE
 a file in which the list of added hills is stored
=HILLS