PLUMED-NEST-TEST-SITE

Project ID: plumID:21.015
Source: MetaD/CBM5/post_processing/calc-weights.dat
Originally used with PLUMED version: 2.5
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

#RESTART
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=721-887

The WHOLEMOLECULES action with label  calculates somethinga1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=798-801 
The CENTER action with label a1 calculates the following quantities:
 Quantity   
 Description  
a1.value
the position of the center of massa2: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=803-807 
The CENTER action with label a2 calculates the following quantities:
 Quantity   
 Description  
a2.value
the position of the center of massa3: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=832-835 
The CENTER action with label a3 calculates the following quantities:
 Quantity   
 Description  
a3.value
the position of the center of massachi: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1-720 


The CENTER action with label achi calculates the following quantities:
 Quantity   
 Description  
achi.value
the position of the center of massp1: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=a1 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The POSITION action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.x
the x-component of the atom position
p1.y
the y-component of the atom position
p1.z
the z-component of the atom positionp2: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=a2 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The POSITION action with label p2 calculates the following quantities:
 Quantity   
 Description  
p2.x
the x-component of the atom position
p2.y
the y-component of the atom position
p2.z
the z-component of the atom positionp3: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=a3 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The POSITION action with label p3 calculates the following quantities:
 Quantity   
 Description  
p3.x
the x-component of the atom position
p3.y
the y-component of the atom position
p3.z
the z-component of the atom positionpchi: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=achi 
NOPBC
 ignore the periodic boundary conditions when calculating distances


The POSITION action with label pchi calculates the following quantities:
 Quantity   
 Description  
pchi.x
the x-component of the atom position
pchi.y
the y-component of the atom position
pchi.z
the z-component of the atom positionc: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=798-801,803-807,832-835 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=1-720 
R_0
The r_0 parameter of the switching function
=0.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=0.7 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100
The COORDINATION action with label c calculates the following quantities:
 Quantity   
 Description  
c.value
the value of the coordinationc: 
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=798-801,803-807,832-835 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=1-720 
R_0
The r_0 parameter of the switching function
=0.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=0.7 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100  
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=0
distx: 
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
=p1.x,p2.x,p3.x,pchi.x 
VAR
the names to give each of the arguments in the function
=a,b,c,y 
FUNC
the function you wish to evaluate
=((y-a)^2+(y-b)^2+(y-c)^2)^0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The MATHEVAL action with label distx calculates the following quantities:
 Quantity   
 Description  
distx.value
an arbitrary function
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
=c,distx
SIGMA
the widths of the Gaussian hills
=0.5,0.5
HEIGHT
the heights of the Gaussian hills
=0.0
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
=50.0
PACE
the frequency for hill addition
=500000000
FILE
 a file in which the list of added hills is stored
=HILLS
GRID_MIN
the lower bounds for the grid
=0.0,0.0
GRID_MAX
the upper bounds for the grid
=75.0,35.0
GRID_BIN
the number of bins for the grid
=375,175
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
... METAD


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialbias: 
REWEIGHT_BIAS
Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored This action has hidden defaults. More details
 
TEMP
the system temperature
=300
The REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the biasbias: 
REWEIGHT_BIAS
Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored This action uses the defaults shown here. More details
 
TEMP
the system temperature
=300  
ARG
 the biases that must be taken into account when reweighting
=*.bias
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=metad.bias 
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
=bias 
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO