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
tested onv2.10
tested onmaster
#
# Avoid too tilted simulation boxes
#

cell:
CELL
Calculate the components of the simulation cell More details
asb_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 values 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 asb_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 values 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 asb_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 values 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
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 bx:
CUSTOM
Calculate a combination of variables using a custom expression. More details
ARG
the values 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
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
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 cx:
CUSTOM
Calculate a combination of variables using a custom expression. More details
ARG
the values 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
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
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 cy:
CUSTOM
Calculate a combination of variables using a custom expression. More details
ARG
the values 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
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
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 #
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 labels of the scalars on which the bias will act
=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
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 values 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
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=100
ARG
the labels of the values that you would like to print to the file
=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
COMMITTOR
Does a committor analysis. More details
...
ARG
the labels of the values which is being used to define the committor surface
=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. This action is a shortcut. 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

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 labels of the values that you would like to print to the file
=drmsd
STRIDE
the frequency with which the quantities of interest should be output
=1000
COMMITTOR
Does a committor analysis. More details
...
ARG
the labels of the values which is being used to define the committor surface
=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