PLUMED-NEST

Project ID: plumID:25.008
Source: mueller/opes/plumed.dat
Originally used with PLUMED version: 2.10
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

The UNITS action with label  calculates somethingpThe POSITION action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.x
scalar
the x-component of the atom position
p.y
scalar
the y-component of the atom position
p.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=1
muellerThe CUSTOM action with label mueller calculates the following quantities:
 Quantity   
 Type   
 Description  
mueller
scalar
an arbitrary function: 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*(-200*exp(-(x-1)^2-10*y^2)-100*exp(-x^2-10*(y-0.5)^2)-170*exp(-6.5*(0.5+x)^2+11*(x+0.5)*(y-1.5)-6.5*(y-1.5)^2)+15*exp(0.7*(1+x)^2+0.6*(x+1)*(y-1)+0.7*(y-1)^2)+146.7)
...
potentialThe BIASVALUE action with label potential calculates the following quantities:
 Quantity   
 Type   
 Description  
potential.bias
scalar
the instantaneous value of the bias potential
potential.mueller_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named mueller: 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=mueller
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 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
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 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


deepTICAThe PYTORCH_MODEL action with label deepTICA calculates the following quantities:
 Quantity   
 Type   
 Description  
deepTICA.node-0
scalar
Model outputs  This is the 0th of these quantities: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=../training/pytorch_models/deeptica_with_koopman_lag1_trans1.ptc ARGthe labels of the values from which the function is calculated=p.x,p.y

dlwallThe LOWER_WALLS action with label dlwall calculates the following quantities:
 Quantity   
 Type   
 Description  
dlwall.bias
scalar
the instantaneous value of the bias potential
dlwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=deepTICA.node-0 KAPPAthe force constant for the wall=1000 ATthe positions of the wall=-1.0
duwallThe UPPER_WALLS action with label duwall calculates the following quantities:
 Quantity   
 Type   
 Description  
duwall.bias
scalar
the instantaneous value of the bias potential
duwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=deepTICA.node-0 KAPPAthe force constant for the wall=1000 ATthe positions of the wall=+1.0

#static bias from metad
metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ...
  ARGthe labels of the scalars on which the bias will act=p.x
  PACEthe frequency for hill addition=5000000
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  HEIGHTthe heights of the Gaussian hills=0.5
  SIGMAthe widths of the Gaussian hills=0.1
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
  FILE a file in which the list of added hills is stored=HILLS_trans1 #for forward transition
  #FILE=HILLS #for back-and-forth transition
...


opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=deepTICA.node-0 PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=20
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=deepTICA.node-0 PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=20  TEMP temperature=-1 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS

PRINTPrint 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=10 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,deepTICA.node-0,opes.*,metad.*

ENDPLUMEDTerminate plumed input. More details