PLUMED-NEST-TEST-SITE

Project ID: plumID:24.011
Source: mueller/iter1/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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITSThis command sets the internal units for the code. More details NATURAL use natural units

# load interface for bias computation
The UNITS action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=./pytorch_model_bias.cpp
#LOAD FILE=./pytorch_model_bias.so

p: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=1

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 positionq: PYTORCH_MODEL_BIASThis action is not part of PLUMED and was included by using a LOAD command More details FILE=../models/model_0.pt ARG=p.x,p.y LAMBDA=1.0 EPSILON=1e-7

mueller: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ...
  FUNCthe function you wish to evaluate=0.15*(146.7-200*exp(-1*(x-1)^2+0*(x-1)*(y-0)-10*(y-0)^2)-100*exp(-1*(x-0)^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))
...

# this is the total bias
The CUSTOM action with label mueller calculates the following quantities:
 Quantity   
 Description  
mueller.value
an arbitrary functionbias: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q.bias-0 varthe names to give each of the arguments in the function=a PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=-a

The CUSTOM action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
an arbitrary functionbiased: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=mueller,bias VARthe names to give each of the arguments in the function=x,y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=x+y 

The CUSTOM action with label biased calculates the following quantities:
 Quantity   
 Description  
biased.value
an arbitrary functionpotential: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=biased

The BIASVALUE action with label potential calculates the following quantities:
 Quantity   
 Description  
potential.bias
the instantaneous value of the bias potential
potential._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filelwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p.x KAPPAthe force constant for the wall=1000 ATthe positions of the wall=-1.3
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p.x KAPPAthe force constant for the wall=1000 ATthe positions of the wall=+1.0

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g STRIDE the frequency with which the quantities of interest should be output=50 FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=p.x,p.y,q.*,bias,mueller,bias

ENDPLUMEDTerminate plumed input. More details