PLUMED-NEST

Project ID: plumID:19.078
Source: meta_reweigthing/6_D/plumed.dat
Originally used with PLUMED version: 2.5-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

# plumed input file
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
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 atomsd2: 
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 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label

The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.x
the x-component of the vector connecting the two atoms
d2.y
the y-component of the vector connecting the two atoms
d2.z
the z-component of the vector connecting the two atomsff: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z 
VAR
the names to give each of the arguments in the function
=x0,x1,x2,x3,x4,x5 
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
=4.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3-1.0)^2-4.0*(x4-1.0)^2-4.0*(x5-1.0)^2)+4.0*exp(-4.0*(x0-1.0)^2-4.0*(x1-1.0)^2-4.0*(x2-1.0)^2-4.0*(x3+1.0)^2-4.0*(x4+1.0)^2-4.0*(x5+1.0)^2)+4.0*exp(-4.0*(x0+1.0)^2-4.0*(x1+1.0)^2-4.0*(x2+1.0)^2-4.0*(x3+1.0)^2-4.0*(x4+1.0)^2-4.0*(x5+1.0)^2)+4.0/(1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+(5.0*x2+5.0)^2+(5.0*x3+5.0)^2+(5.0*x4+5.0)^2+(5.0*x5+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3+5.0)^2+(5.0*x4+5.0)^2+(5.0*x5+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+(5.0*x2-5.0)^2+(5.0*x3-5.0)^2+(5.0*x4-5.0)^2+(5.0*x5-5.0)^2+1)+1.0/((-2.04124145231931*x0-0.591751709536137*x1-0.591751709536137*x2-0.591751709536137*x3-0.591751709536137*x4+4.40824829046386*x5)^2.0+(-2.04124145231931*x0-0.591751709536137*x1-0.591751709536137*x2-0.591751709536137*x3+4.40824829046386*x4-0.591751709536137*x5)^2.0+(-2.04124145231931*x0-0.591751709536137*x1-0.591751709536137*x2+4.40824829046386*x3-0.591751709536137*x4-0.591751709536137*x5)^2.0+(-2.04124145231931*x0-0.591751709536137*x1+4.40824829046386*x2-0.591751709536137*x3-0.591751709536137*x4-0.591751709536137*x5)^2.0+(-2.04124145231931*x0+4.40824829046386*x1-0.591751709536137*x2-0.591751709536137*x3-0.591751709536137*x4-0.591751709536137*x5)^2.0+(0.408248290463863*x0+0.408248290463863*x1+0.408248290463863*x2+0.408248290463863*x3+0.408248290463863*x4+0.408248290463863*x5)^8.0)+1.0/((5.0*x3+5.0)^2.0+(5.0*x4+5.0)^2.0+(5.0*x5+5.0)^2.0+(-2.88675134594813*x0-1.05662432702594*x1+3.94337567297406*x2)^2.0+(-2.88675134594813*x0+3.94337567297406*x1-1.05662432702594*x2)^2.0+(0.577350269189626*x0+0.577350269189626*x1+0.577350269189626*x2)^8.0)+1.0/((5.0*x1-5.0)^2.0+(5.0*x2-5.0)^2.0+(0.577350269189626*x3+0.577350269189626*x4+0.577350269189626*x5)^8.0+(-2.88675134594813*x0-1.66666666666667*x3-1.66666666666667*x4+3.33333333333333*x5+2.88675134594813)^2.0+(-2.88675134594813*x0-1.66666666666667*x3+3.33333333333333*x4-1.66666666666667*x5+2.88675134594813)^2.0+(-2.88675134594813*x0+3.33333333333333*x3-1.66666666666667*x4-1.66666666666667*x5+2.88675134594813)^2.0


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

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. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z 
PACE
the frequency for hill addition
=500
SIGMA
the widths of the Gaussian hills
=0.1,0.1,0.1,0.1,0.1,0.1 
HEIGHT
the heights of the Gaussian hills
=4.0 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=3 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=1
...

The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potential
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 
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
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
=1,2,3