PLUMED-NEST

Project ID: plumID:23.022
Source: results/unsupervised/iter_14/data/plumed.dat
Originally used with PLUMED version: 2.9
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units

p: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1

# define modified Muller Brown potential
The POSITION action with label p calculates the following quantities:
 Quantity   
 Description  
p.x
the x-component of the atom position
p.y
the y-component of the atom position
p.z
the z-component of the atom positionene: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y 
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
=0.15*(146.7-280*exp(-15*(x-1)^2+0*(x-1)*(y-0)-10*(y-0)^2)-170*exp(-1*(x-0.2)^2+0*(x-0)*(y-0.5)-10*(y-0.5)^2)-170*exp(-6.5*(x+0.5)^2+11*(x+0.5)*(y-1.5)-6.5*(y-1.5)^2)+15*exp(0.7*(x+1)^2+0.6*(x+1)*(y-1)+0.7*(y-1)^2
...

pot: 
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
=ene

# load deep cv pytorch model
The BIASVALUE action with label pot calculates the following quantities:
 Quantity   
 Description  
pot.bias
the instantaneous value of the bias potential
pot._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filecv: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=../model_autoencoder_14.pt 
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y 

# apply bias
The PYTORCH_MODEL action with label cv calculates the following quantities:
 Quantity   
 Description  
cv.node
Model outputsopes: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cv.node-0 
PACE
the frequency for kernel deposition
=500 
BARRIER
the free energy barrier to be overcome
=16

The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
PRINT
Print quantities to a file. More details
 
FMT
the format that should be used to output real numbers
=%g 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y,cv.*,opes

ENDPLUMED
Terminate plumed input. More details