PLUMED-NEST-TEST-SITE

Project ID: plumID:22.034
Source: plumed_meta.dat
Originally used with PLUMED version: 2.4
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

#
# Avoid too tilted simulation boxes
#

cell: 
CELL
Calculate the components of the simulation cell More details
The CELL action with label cell calculates the following quantities:
 Quantity   
 Description  
cell.ax
the ax component of the cell matrix
cell.ay
the ay component of the cell matrix
cell.az
the az component of the cell matrix
cell.bx
the bx component of the cell matrix
cell.by
the by component of the cell matrix
cell.bz
the bz component of the cell matrix
cell.cx
the cx component of the cell matrix
cell.cy
the cy component of the cell matrix
cell.cz
the cz component of the cell matrixasb_bx: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=cell.bx,cell.ax 
FUNC
the function you wish to evaluate
=abs(x)-0.5*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label asb_bx calculates the following quantities:
 Quantity   
 Description  
asb_bx.value
an arbitrary functionasb_cx: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=cell.cx,cell.ax 
FUNC
the function you wish to evaluate
=abs(x)-0.5*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label asb_cx calculates the following quantities:
 Quantity   
 Description  
asb_cx.value
an arbitrary functionasb_cy: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=cell.cy,cell.by 
FUNC
the function you wish to evaluate
=abs(x)-0.5*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label asb_cy calculates the following quantities:
 Quantity   
 Description  
asb_cy.value
an arbitrary function
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
=asb_bx,asb_cx,asb_cy
AT
the positions of the wall
=0.0,0.0,0.0
KAPPA
the force constant for the wall
=1000000,1000000,1000000
EXP
 the powers for the walls
=2,2,2
EPS
 the values for s_i in the expression for a wall
=1,1,1
OFFSET
 the offset for the start of the wall
=0.05,0.05,0.05
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ASB
... UPPER_WALLS

#
# Set limits for non-diagonal elements of the simulation box
#

# Box Angles
# cell: CELL
The UPPER_WALLS action with label ASB calculates the following quantities:
 Quantity   
 Description  
ASB.bias
the instantaneous value of the bias potential
ASB.force2
the instantaneous value of the squared force due to this bias potentialbx: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=cell.bx 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Wall
The CUSTOM action with label bx calculates the following quantities:
 Quantity   
 Description  
bx.value
an arbitrary function
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
=bx
AT
the positions of the wall
=5.75
KAPPA
the force constant for the wall
=10000
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
=0.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bx_upper
... UPPER_WALLS

# Wall
The UPPER_WALLS action with label bx_upper calculates the following quantities:
 Quantity   
 Description  
bx_upper.bias
the instantaneous value of the bias potential
bx_upper.force2
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
=bx
AT
the positions of the wall
=-5.75
KAPPA
the force constant for the wall
=10000
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
=0.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bx_lower
... LOWER_WALLS

# Box Angles
# cell: CELL
The LOWER_WALLS action with label bx_lower calculates the following quantities:
 Quantity   
 Description  
bx_lower.bias
the instantaneous value of the bias potential
bx_lower.force2
the instantaneous value of the squared force due to this bias potentialcx: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=cell.cx 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Wall
The CUSTOM action with label cx calculates the following quantities:
 Quantity   
 Description  
cx.value
an arbitrary function
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
=cx
AT
the positions of the wall
=5.75
KAPPA
the force constant for the wall
=10000
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
=0.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cx_upper
... UPPER_WALLS

# Wall
The UPPER_WALLS action with label cx_upper calculates the following quantities:
 Quantity   
 Description  
cx_upper.bias
the instantaneous value of the bias potential
cx_upper.force2
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
=cx
AT
the positions of the wall
=-5.75
KAPPA
the force constant for the wall
=10000
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
=0.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cx_lower
... LOWER_WALLS

# Box Angles
# cell: CELL
The LOWER_WALLS action with label cx_lower calculates the following quantities:
 Quantity   
 Description  
cx_lower.bias
the instantaneous value of the bias potential
cx_lower.force2
the instantaneous value of the squared force due to this bias potentialcy: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=cell.cy 
FUNC
the function you wish to evaluate
=x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Wall
The CUSTOM action with label cy calculates the following quantities:
 Quantity   
 Description  
cy.value
an arbitrary function
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
=cy
AT
the positions of the wall
=5.75
KAPPA
the force constant for the wall
=10000
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
=0.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cy_upper
... UPPER_WALLS

# Wall
The UPPER_WALLS action with label cy_upper calculates the following quantities:
 Quantity   
 Description  
cy_upper.bias
the instantaneous value of the bias potential
cy_upper.force2
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
=cy
AT
the positions of the wall
=-5.75
KAPPA
the force constant for the wall
=10000
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
=0.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cy_lower
... LOWER_WALLS

#
# Metadynamics Parameters
#

The LOWER_WALLS action with label cy_lower calculates the following quantities:
 Quantity   
 Description  
cy_lower.bias
the instantaneous value of the bias potential
cy_lower.force2
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
=meta
ARG
the input for this action is the scalar output from one or more other actions
=bx,cx,cy
PACE
the frequency for hill addition
=1000
HEIGHT
the heights of the Gaussian hills
=2.0
SIGMA
the widths of the Gaussian hills
=0.1,0.1,0.1
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
BIASFACTOR
use well tempered metadynamics and use this bias factor
=200
GRID_MIN
the lower bounds for the grid
=-6.0,-6.0,-6.0
GRID_MAX
the upper bounds for the grid
=6.0,6.0,6.0
GRID_BIN
the number of bins for the grid
=240,240,240
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
FILE
 a file in which the list of added hills is stored
=HILLS
... 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)rct_mol: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the input to this function
=meta.rct 
FUNC
the function you wish to evaluate
=x/252.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO # 252 = number of molecules

The MATHEVAL action with label rct_mol calculates the following quantities:
 Quantity   
 Description  
rct_mol.value
an arbitrary function
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
ARG
the input for this action is the scalar output from one or more other actions
=bx,cx,cy,meta.bias,meta.rbias,meta.rct,rct_mol,ASB.bias,bx_lower.bias,bx_upper.bias,cx_lower.bias,cx_upper.bias,cy_lower.bias,cy_upper.bias 
FILE
the name of the file on which to output these quantities
=plumed_meta_COLVAR

# 
# Committor
#

# Stop simulation after energy cutoff is reached
The PRINT action with label  calculates something
COMMITTOR
Does a committor analysis. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=rct_mol
STRIDE
 the frequency with which the CVs are analyzed
=100000
BASIN_LL1
List of lower limits for basin #
=4.0
BASIN_UL1
List of upper limits for basin #
=14.0
... COMMITTOR

# Stop simulation after the DRMSD cutoff is reached
DRMSD
Calculate the distance RMSD with respect to a reference structure. More details
 ...
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=plumed_meta.pdb 
LOWER_CUTOFF
only pairs of atoms further than LOWER_CUTOFF are considered in the calculation
=0.1 
UPPER_CUTOFF
only pairs of atoms closer than UPPER_CUTOFF are considered in the calculation
=0.8
TYPE
 what kind of DRMSD would you like to calculate
=INTER-DRMSD
LABEL
a label for the action so that its output can be referenced in the input to other actions
=drmsd
... DRMSD

The DRMSD action with label drmsd calculates the following quantities:
 Quantity   
 Description  
drmsd.value
the DRMSD distance between the instantaneous structure and the reference structure
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=plumed_meta_DRMSD 
ARG
the input for this action is the scalar output from one or more other actions
=drmsd 
STRIDE
 the frequency with which the quantities of interest should be output
=1000

COMMITTOR
Does a committor analysis. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=drmsd
  
STRIDE
 the frequency with which the CVs are analyzed
=100000
  
BASIN_LL1
List of lower limits for basin #
=0.5
  
BASIN_UL1
List of upper limits for basin #
=10.5
... COMMITTOR