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
tested onv2.9
tested onmaster
#
UNITS
This command sets the internal units for the code. More details
NATURAL
use natural units
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
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label

ff:
MATHEVAL
An alias to the ef CUSTOM function. 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
bb:
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
mt:
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
=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 ...
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