PLUMED-NEST

Project ID: plumID:23.010
Source: plumed.dat
Originally used with PLUMED version: 2.5.3
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

#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
=1 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-4903

d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,3931 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 # ADR(N) and TRP(CA)

###FUNNEL_PARAMETERS###
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.x
the x-component of the vector connecting the two atoms
d1.y
the y-component of the vector connecting the two atoms
d1.z
the z-component of the vector connecting the two atomss_cent: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUES
the numbers that are in your constant value
=4.0                                           # INFLEXION
The CONSTANT action with label s_cent calculates a scalar quantitybeta_cent: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUES
the numbers that are in your constant value
=2.0                                        # STEEPNESS
The CONSTANT action with label beta_cent calculates a scalar quantitywall_width: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUES
the numbers that are in your constant value
=1.5                                       # WIDTH (h)
The CONSTANT action with label wall_width calculates a scalar quantitywall_buffer: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUES
the numbers that are in your constant value
=0.15                                     # BUFFER (f, total width = WIDTH + BUFFER)
The CONSTANT action with label wall_buffer calculates a scalar quantitylwall: 
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
=0.2 
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           # Lower Wall (the starting point of the funnel)
uwall: 
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 
AT
the positions of the wall
=3.5 
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           # Upper Wall (the ending point of the funnel)
       
###########CALCULATE FUNNEL#######
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

########BIAS OF THE WALL######
wall_height: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=100.0
The CONSTANT action with label wall_height calculates a scalar quantitywall_steepness: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=500.0

#######PROYECTION DXY##########
The CONSTANT action with label wall_steepness calculates a scalar quantity
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

#######DEFINE_POTENTIAL#######
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,wall_height,wall_steepness,wall_center
        
VAR
the names to give each of the arguments in the function
=z,h,b,zc
        
FUNC
the function you wish to evaluate
=h*(1.-(1./(1.+exp(b*(z-zc
        
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL

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

########DEFINE_METAD###########
The BIASVALUE action with label finalbias calculates the following quantities:
 Quantity   
 Description  
finalbias.bias
the instantaneous value of the bias potential
finalbias._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
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
=meta 
ARG
the input for this action is the scalar output from one or more other actions
=d1.z
        
SIGMA
the widths of the Gaussian hills
=0.1 
HEIGHT
the heights of the Gaussian hills
=5
        
PACE
the frequency for hill addition
=500 
FILE
 a file in which the list of added hills is stored
=../HILLS
        
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.0
        
GRID_MIN
the lower bounds for the grid
=-1.0 
GRID_MAX
the upper bounds for the grid
=5.0 
GRID_BIN
the number of bins for the grid
=200
        
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
        
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD

The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.bias
the instantaneous value of the bias potential
meta.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
meta.rct
the reweighting factor $c(t)$
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