Project ID: plumID:19.042
Source: 2_class/meta/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
#RESTART
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
energy:
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
d2:
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
d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=3,4
NOPBC
ignore the periodic boundary conditions when calculating distances
d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=4,5
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
=5,6
NOPBC
ignore the periodic boundary conditions when calculating distances
d6:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=6,1
NOPBC
ignore the periodic boundary conditions when calculating distances

comb1:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6
COEFFICIENTS
the coefficients of the arguments in your function
=0.182,-0.456,0.106,-0.602,0.065,-0.617
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
=d4
AT
the positions of the wall
=+5.0
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
=d6
AT
the positions of the wall
=+5.0
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
metad:
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
=comb1
PACE
the frequency for hill addition
=100
HEIGHT
the heights of the Gaussian hills
=5.0
SIGMA
the widths of the Gaussian hills
=0.2
GRID_MIN
the lower bounds for the grid
=-15
GRID_MAX
the upper bounds for the grid
=15
GRID_BIN
the number of bins for the grid
=2000
FILE
a file in which the list of added hills is stored
=HILLS
BIASFACTOR
use well tempered metadynamics and use this bias factor
=80
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
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
PRINT
Print quantities to a file. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5,d6,comb1,metad
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 ... PRINT