PLUMED-NEST

Project ID: plumID:19.043
Source: 3_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

#
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, fs
RESTART
Activate restart. 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
 
The DISTANCE action with label d1 calculates a scalar quantityd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,3 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d2 calculates a scalar quantityd3: 
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

The DISTANCE action with label d3 calculates a scalar quantityhc: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=1 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=4,5 
LESS_THAN
calculate the number of variables that are less than a certain target value
={RATIONAL R_0=2.0 NN=6 MM=12}

d4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,4 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d4 calculates a scalar quantityd5: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,5 
NOPBC
 ignore the periodic boundary conditions when calculating distances

The DISTANCE action with label d5 calculates a scalar quantity
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
=+7.5  
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
=d2 
AT
the positions of the wall
=+7.5  
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
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
=d3 
AT
the positions of the wall
=+7.5  
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_3
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
=+1.25 
KAPPA
the force constant for the wall
=500.0 
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_4
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
=+1.25 
KAPPA
the force constant for the wall
=500.0 
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_5

comb1:  
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1,d2,d3 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.555,-0.810,0.190 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
comb2:  
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1,d2,d3 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.600,0.234,-0.765 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

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
=comb1,comb2
 
PACE
the frequency for hill addition
=50 
 
HEIGHT
the heights of the Gaussian hills
=2.0 
 
SIGMA
the widths of the Gaussian hills
=0.2 
 
GRID_MIN
the lower bounds for the grid
=-15,-15
 
GRID_MAX
the upper bounds for the grid
=15,15
 
GRID_BIN
the number of bins for the grid
=300,300
 
FILE
 a file in which the list of added hills is stored
=HILLS
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=25  
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0 
 
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=GEOM
... METAD


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
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
=10
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,d2,d3,comb1,comb2,d4,d5,metad