PLUMED-NEST

Project ID: plumID:19.078
Source: meta_reweigthing/3_D/plumed_reweight.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 for reweigthing
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 atomsff: 
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

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 
PACE
the frequency for hill addition
=1
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
...

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
=bias.reweight 
STRIDE
 the frequency with which the quantities of interest should be output
=10
rw: 
REWEIGHT_BIAS
Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details
 
ARG
 the biases that must be taken into account when reweighting
=mt.bias 
TEMP
the system temperature
=1  # This is the inverse of boltzmann's constant in kJ mol-1
The REWEIGHT_BIAS action with label rw calculates a scalar quantitycc: 
COLLECT_FRAMES
This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object More details
 
ARG
the arguments you would like to collect
=d1.x,d1.y,d1.z 
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=rw 
STRIDE
 the frequency with which data should be stored for analysis
=10
it: 
ITRE
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=cc.logweights TEMP=1 MAXITER=20
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=it 
FILE
the name of the file on which to output these quantities
=c_t.dat 
FMT
the format that should be used to output real numbers
=%8.4f