Project ID: plumID:19.054
Source: plumed.dat
Originally used with PLUMED version: 2.3
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
tested onv2.9
tested onmaster
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
TIME
the units of time
=0.001 #Amstroeng, hartree, fs
ene:
ENERGY
Calculate the total potential energy of the simulation box. More details
d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1,2
NOPBC
ignore the periodic boundary conditions when calculating distances
d5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1,6
NOPBC
ignore the periodic boundary conditions when calculating distances

c1:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d5
COEFFICIENTS
the coefficients of the arguments in your function
=0.500,-0.500
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
h1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2,3
NOPBC
ignore the periodic boundary conditions when calculating distances
h2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2,4
NOPBC
ignore the periodic boundary conditions when calculating distances
h3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2,5
NOPBC
ignore the periodic boundary conditions when calculating distances

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
AT
the positions of the wall
=+4.0
KAPPA
the force constant for the wall
=150.0
EXP
the powers for the walls
=2
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_1
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
=d5
AT
the positions of the wall
=+4.0
KAPPA
the force constant for the wall
=150.0
EXP
the powers for the walls
=2
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_2
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
=h1
AT
the positions of the wall
=+1.7
KAPPA
the force constant for the wall
=150.0
EXP
the powers for the walls
=2
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall_1
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
=h2
AT
the positions of the wall
=+1.7
KAPPA
the force constant for the wall
=150.0
EXP
the powers for the walls
=2
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall_2
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
=h3
AT
the positions of the wall
=+1.7
KAPPA
the force constant for the wall
=150.0
EXP
the powers for the walls
=2
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall_3
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
=metad
ARG
the input for this action is the scalar output from one or more other actions
=c1
PACE
the frequency for hill addition
=50
HEIGHT
the heights of the Gaussian hills
=2.0
SIGMA
the widths of the Gaussian hills
=0.1
FILE
a file in which the list of added hills is stored
=HILLS
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
CALC_RCT
calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
GRID_MIN
the lower bounds for the grid
=-4
GRID_MAX
the upper bounds for the grid
=+4
GRID_BIN
the number of bins for the grid
=1000 ... METAD
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=1
FILE
the name of the file on which to output these quantities
=COLVAR
ARG
the input for this action is the scalar output from one or more other actions
=d1,d5,c1,metad.*,ene
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
STRIDE
the frequency with which all the open files should be flushed
=1