PLUMED-NEST

Project ID: plumID:23.022
Source: results/timelagged/deepTICA/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 filetica: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=../model_deepTICA.pt 
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y

# apply static bias from previous sim
The PYTORCH_MODEL action with label tica calculates the following quantities:
 Quantity   
 Description  
tica.node
Model outputsstatic: 
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
=p.y ...
    
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=YES
    
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=../../../../input_data/timelagged/opes-y/State.data
    
BARRIER
the free energy barrier to be overcome
=16
    
PACE
the frequency for kernel deposition
=10000000
...

The OPES_METAD action with label static calculates the following quantities:
 Quantity   
 Description  
static.bias
the instantaneous value of the bias potential
static.rct
estimate of c(t)
static.zed
estimate of Z_n
static.neff
effective sample size
static.nker
total number of compressed kernels used to represent the biaslwall_x: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=p.x 
KAPPA
the force constant for the wall
=1000 
AT
the positions of the wall
=-1.3
uwall_x: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=p.x 
KAPPA
the force constant for the wall
=1000 
AT
the positions of the wall
=+1.2
lwall_y: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=p.y 
KAPPA
the force constant for the wall
=1000 
AT
the positions of the wall
=-0.4
uwall_y: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=p.y 
KAPPA
the force constant for the wall
=1000 
AT
the positions of the wall
=+2.0

# apply bias
opes: 
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
=tica.node-0 
PACE
the frequency for kernel deposition
=200 
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
=200 
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,tica.*,opes.*,static

ENDPLUMED
Terminate plumed input. More details