PLUMED-NEST-TEST-SITE

Project ID: plumID:21.021
Source: meta_inputs/meta_3d/plumed.dat
Originally used with PLUMED version: 2.7-mod
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

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UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units
The UNITS action with label  calculates somethingd1: 
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 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label

The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.x
the x-component of the vector connecting the two atoms
d1.y
the y-component of the vector connecting the two atoms
d1.z
the z-component of the vector connecting the two atoms
d1.value
the DISTANCE between this pair of atomsff: 
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
=d1.x,d1.y,d1.z 
VAR
the names to give each of the arguments in the function
=x0,x1,x2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=30.0*exp(-4.0*(x0-1)^2-4.0*(x1-1)^2-4.0*(x2+1)^2)+30.0*exp(-4.0*(x0-1)^2-4.0*(x1+1)^2-4.0*(x2-1)^2)+30.0*exp(-4.0*(x0-1)^2-4.0*(x1+1)^2-4.0*(x2+1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1-1)^2-4.0*(x2-1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1+1)^2-4.0*(x2-1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1+1)^2-4.0*(x2+1)^2)+30.0/(1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+(5.0*x2+5.0)^2+1)+1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+(5.0*x2-5.0)^2+1)+1.0/((5.0*x0+5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1+5.0)^2+(5.0*x2+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1+5.0)^2+(5.0*x2-5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2+5.0)^2+1)+1.0/((10.0*x0-10.0)^2+(0.5*x1-0.5*x2)^8+(7.0710678*x1+7.0710678*x2)^2)+1.0/((0.5*x0-0.5*x2)^8+(7.0710678*x0+7.0710678*x2)^2+(10.0*x1-10.0)^2)+1.0/((-7.0710678*x0-7.0710678*x1)^2+(0.288675134189626*x0-0.288675134189626*x1-0.408248289205788*x2)^8+(5.0*x0-5.0*x1+7.0710678*x2)^2)+1.0/(1.0*x2^8+(10.0*x0+10.0)^2+(10.0*x1+10.0)^2)+1.0/(1.0*x0^8+(10.0*x1+10.0)^2+(10.0*x2+10.0)^2)+1.0/(1.0*x0^8+(10.0*x1+10.0)^2+(10.0*x2-10.0)^2

The MATHEVAL action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.value
an arbitrary functionbb: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ff

The BIASVALUE action with label bb calculates the following quantities:
 Quantity   
 Description  
bb.bias
the instantaneous value of the bias potential
bb._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filemt: 
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=d1.x,d1.y,d1.z 
PACE
the frequency for hill addition
=500
GRID_MIN
the lower bounds for the grid
=-1.75,-1.75,-1.75 
GRID_MAX
the upper bounds for the grid
=1.75,1.75,1.75 
GRID_BIN
the number of bins for the grid
=300,300,300
HEIGHT
the heights of the Gaussian hills
=2.0 
SIGMA
the widths of the Gaussian hills
=0.05,0.05,0.05 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=1.0
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
#REWEIGHTING_NGRID=100,100,100
...
The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potential
mt.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
mt.rct
the reweighting factor c(t)mt: 
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=d1.x,d1.y,d1.z 
PACE
the frequency for hill addition
=500
GRID_MIN
the lower bounds for the grid
=-1.75,-1.75,-1.75 
GRID_MAX
the upper bounds for the grid
=1.75,1.75,1.75 
GRID_BIN
the number of bins for the grid
=300,300,300
HEIGHT
the heights of the Gaussian hills
=2.0 
SIGMA
the widths of the Gaussian hills
=0.05,0.05,0.05 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=1.0
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
#REWEIGHTING_NGRID=100,100,100
 
FILE
 a file in which the list of added hills is stored
=HILLS
...

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=mt.bias,mt.rct,mt.rbias 
FILE
the name of the file on which to output these quantities
=rr.bias_500 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=mt.bias,mt.rct,mt.rbias 
FILE
the name of the file on which to output these quantities
=rr.bias_50 
STRIDE
 the frequency with which the quantities of interest should be output
=50
DUMPATOMS
Dump selected atoms on a file. More details
 
STRIDE
 the frequency with which the atoms should be output
=500 
FILE
file on which to output coordinates; extension is automatically detected
=traj.xyz 
ATOMS
the atom indices whose positions you would like to print out
=1,2