Project ID: plumID:19.048
Source: A1_ZMA.dat
Originally used with PLUMED version: 2.3.1
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
tested onv2.9
tested onmaster
#RESTART 
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
STRIDE
the frequency with which molecules are reassembled
=1000
ENTITY0
the atoms that make up a molecule that you wish to align
=1-4862
lig:
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
=4878,4880 d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=3877,lig
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
bridge:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2595,4181
MATHEVAL
An alias to the ef CUSTOM function. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dxy
ARG
the input to this function
=d1.x,d1.y
VAR
the names to give each of the arguments in the function
=ax,ay
FUNC
the function you wish to evaluate
=(sqrt(ax*ax+ay*ay
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... MATHEVAL
############################################################ s_cent:
CONSTANT
Create a constant value that can be passed to actions More details
VALUE
the single number that you would like to store
=4 beta_cent:
CONSTANT
Create a constant value that can be passed to actions More details
VALUE
the single number that you would like to store
=2 wall_width:
CONSTANT
Create a constant value that can be passed to actions More details
VALUE
the single number that you would like to store
=1.6 wall_buffer:
CONSTANT
Create a constant value that can be passed to actions More details
VALUE
the single number that you would like to store
=0.15
MATHEVAL
An alias to the ef CUSTOM function. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall_center
ARG
the input to this function
=d1.z,s_cent,beta_cent,wall_width,wall_buffer
VAR
the names to give each of the arguments in the function
=s,sc,b,h,f
FUNC
the function you wish to evaluate
=h*(1./(1.+exp(b*(s-sc))))+f
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... MATHEVAL
scaling:
CONSTANT
Create a constant value that can be passed to actions More details
VALUES
the numbers that are in your constant value
=1.0 spring:
CONSTANT
Create a constant value that can be passed to actions More details
VALUES
the numbers that are in your constant value
=3000.0
MATHEVAL
An alias to the ef CUSTOM function. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall_bias
ARG
the input to this function
=dxy,spring,wall_center,scaling
VAR
the names to give each of the arguments in the function
=z,k,zc,sf
FUNC
the function you wish to evaluate
=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sf
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... MATHEVAL
############################################################
meta:
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
=d1.z,bridge
SIGMA
the widths of the Gaussian hills
=0.1,0.0333
HEIGHT
the heights of the Gaussian hills
=1
PACE
the frequency for hill addition
=500
FILE
a file in which the list of added hills is stored
=HILLS
GRID_MIN
the lower bounds for the grid
=-0.5,-0.5
GRID_MAX
the upper bounds for the grid
=5.5,2.5
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.05,0.01665
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
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.z,bridge
AT
the positions of the wall
=5.0,1.75
KAPPA
the force constant for the wall
=1500.0,1500.0
EXP
the powers for the walls
=2,2
EPS
the values for s_i in the expression for a wall
=1,1
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.z
AT
the positions of the wall
=0.5
KAPPA
the force constant for the wall
=1500.0
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall
finalbias:
BIASVALUE
Takes the value of one variable and use it as a bias More details
ARG
the input for this action is the scalar output from one or more other actions
=wall_bias
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
=500
FILE
the name of the file on which to output these quantities
=COLVAR