PLUMED-NEST

Project ID: plumID:22.045
Source: plumed-METAD.dat
Originally used with PLUMED version: 2.4.3
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

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-4053

DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1912,4012  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d0
The DISTANCE action with label d0 calculates a scalar quantity
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3966,4009  
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
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3082,1912  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hiser

The DISTANCE action with label hiser calculates a scalar quantity
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=4013,1912  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=de
The DISTANCE action with label de calculates a scalar quantity
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=4013,1916  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hole
The DISTANCE action with label hole calculates a scalar quantity
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=4013,842   
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hole2

The DISTANCE action with label hole2 calculates a scalar quantity
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
=hole,hole2 
PACE
the frequency for hill addition
=400 
HEIGHT
the heights of the Gaussian hills
=0.1 
SIGMA
the widths of the Gaussian hills
=0.05,0.05 
FILE
 a file in which the list of added hills is stored
=HILLS 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=30.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0 
GRID_MIN
the lower bounds for the grid
=-1,-1 
GRID_MAX
the upper bounds for the grid
=2,2
 ... METAD

The METAD action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the 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
=hole,hole2 
AT
the positions of the wall
=0.6,0.6 
KAPPA
the force constant for the wall
=15000,15000 
EXP
 the powers for the walls
=2,2 
EPS
 the values for s_i in the expression for a wall
=1,1 
OFFSET
 the offset for the start of the wall
=0,0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall
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
=d1 
AT
the positions of the wall
=2.3 
KAPPA
the force constant for the wall
=550  
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

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
   
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