PLUMED-NEST

Project ID: plumID:22.025
Source: t0.700/p0.14000-fes/plumed.inp
Originally used with PLUMED version: 2.8
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

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../code/ReweightGeomFES.cpp
 
The LOAD action with label  calculates somethingUNITSThis command sets the internal units for the code. More details NATURAL use natural units

VOLUMECalculate the volume of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=vol
The VOLUME action with label vol calculates the following quantities:
 Quantity   
 Description  
vol.value
the volume of simulation boxCUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=vol FUNCthe function you wish to evaluate=x/4096 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=molvol

The CUSTOM action with label molvol calculates the following quantities:
 Quantity   
 Description  
molvol.value
an arbitrary functionCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=coord
  SPECIESthis keyword is used for colvars such as coordination number=1-4096
  SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=1.6 D_MAX=2.5}
  LESS_THANcalculate the number of variables that are less than a certain target value={RATIONAL R_0=5 D_MAX=7.5 NN=12}
  LOWMEM this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER

The COORDINATIONNUMBER action with label coord calculates the following quantities:
 Quantity   
 Description  
coord.lessthan
the number of colvars that have a value less than a threshold
coord.value
the coordination numbers of the specified atomsUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=molvol ATthe positions of the wall=1.55 KAPPAthe force constant for the wall=1e5 LABELa label for the action so that its output can be referenced in the input to other actions=wall1
The UPPER_WALLS action with label wall1 calculates the following quantities:
 Quantity   
 Description  
wall1.bias
the instantaneous value of the bias potential
wall1.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=coord.lessthan ATthe positions of the wall=1e5 KAPPAthe force constant for the wall=1.0 STRIDEthe frequency with which the forces due to the bias should be calculated=10 LABELa label for the action so that its output can be referenced in the input to other actions=wall2

# ANN BIAS
The UPPER_WALLS action with label wall2 calculates the following quantities:
 Quantity   
 Description  
wall2.bias
the instantaneous value of the bias potential
wall2.force2
the instantaneous value of the squared force due to this bias potentialANNCalculates the ANN-function. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=fesfit
  ARGthe labels of the values from which the function is calculated=molvol
  NUM_LAYERSnumber of layers of the neural network=4
  NUM_NODESnumbers of nodes in each layer of the neural network=1,1,12,1
  ACTIVATIONSactivation functions for the neural network=Linear,Tanh,Linear
  WEIGHTS0flattened weight arrays connecting adjacent layers, WEIGHTS0 represents flattened weight array connecting layer 0 and layer 1, WEIGHTS1 represents flattened weight array connecting layer 1 and layer 2, =10.0
  WEIGHTS1flattened weight arrays connecting adjacent layers, WEIGHTS0 represents flattened weight array connecting layer 0 and layer 1, WEIGHTS1 represents flattened weight array connecting layer 1 and layer 2, =-4.02106452,4.949982,1.80240797,4.46537074,4.49943175,-3.90593335,-0.85355746,-1.24826019,-2.05655944,-3.67396211,4.09918394,0.79585369
  WEIGHTS2flattened weight arrays connecting adjacent layers, WEIGHTS0 represents flattened weight array connecting layer 0 and layer 1, WEIGHTS1 represents flattened weight array connecting layer 1 and layer 2, =1.79597931,2.7875915,-0.67711734,2.83836018,2.04242457,2.8062143,0.45558524,3.35225743,3.80568881,-1.70005164,1.89059126,-2.03214932
  BIASES0bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, =-14.0
  BIASES1bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, =2.28440845e-01,-4.80218169e+00,-6.76891150e-01,-4.21579617e+00,-2.54626376e+00,2.16008837e-01,-8.46909047e-04,1.77873690e+00,4.13324665e+00,2.19442795e+00,-3.71693207e+00,-8.48992764e-01
  BIASES2bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, =1.39189613
... ANN

The ANN action with label fesfit calculates the following quantities:
 Quantity   
 Description  
fesfit.node
components of ANN outputsCUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=fesfit.node-0 FUNCthe function you wish to evaluate=-1.0*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=wt
The CUSTOM action with label wt calculates the following quantities:
 Quantity   
 Description  
wt.value
an arbitrary functionBIASVALUETakes 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=wt LABELa label for the action so that its output can be referenced in the input to other actions=b1

The BIASVALUE action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileREWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details TEMPthe system temperature=0.700 ARG the biases that must be taken into account when reweighting=b1.bias LABELa label for the action so that its output can be referenced in the input to other actions=bias
The REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the biasREWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details TEMP=0.700 ARG=coord.lessthan LABEL=gd1

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=coord.lessthan
  GRID_MIN the lower bounds for the grid=-1
  GRID_MAX the upper bounds for the grid=20
  GRID_BINthe number of bins for the grid=1050
  BANDWIDTHthe bandwidths for kernel density esimtation=0.2
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias
  STRIDE the frequency with which to store data for averaging=10
  LABELa label for the action so that its output can be referenced in the input to other actions=hh
... HISTOGRAM

The HISTOGRAM action with label hh calculates the following quantities:
 Quantity   
 Description  
hh.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=coord.lessthan
  GRID_MIN the lower bounds for the grid=-1
  GRID_MAX the upper bounds for the grid=20
  GRID_BINthe number of bins for the grid=1050
  BANDWIDTHthe bandwidths for kernel density esimtation=0.2
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,gd1
  STRIDE the frequency with which to store data for averaging=10
  LABELa label for the action so that its output can be referenced in the input to other actions=hhg
... HISTOGRAM

The HISTOGRAM action with label hhg calculates the following quantities:
 Quantity   
 Description  
hhg.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=molvol
  GRID_MIN the lower bounds for the grid=1.40
  GRID_MAX the upper bounds for the grid=1.60
  GRID_BINthe number of bins for the grid=400
  BANDWIDTHthe bandwidths for kernel density esimtation=0.005
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias
  LABELa label for the action so that its output can be referenced in the input to other actions=hhd
... HISTOGRAM

The HISTOGRAM action with label hhd calculates the following quantities:
 Quantity   
 Description  
hhd.value
the estimate of the histogram as a function of the argument that was obtainedCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hh  TEMPthe temperature at which you are operating=0.700 LABELa label for the action so that its output can be referenced in the input to other actions=ff
The CONVERT_TO_FES action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hhg TEMPthe temperature at which you are operating=0.700 LABELa label for the action so that its output can be referenced in the input to other actions=ffg
The CONVERT_TO_FES action with label ffg calculates the following quantities:
 Quantity   
 Description  
ffg.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hhd TEMPthe temperature at which you are operating=0.700 LABELa label for the action so that its output can be referenced in the input to other actions=ffd

The CONVERT_TO_FES action with label ffd calculates the following quantities:
 Quantity   
 Description  
ffd.value
the free energy surfaceDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=ff  FILE the file on which to write the grid=fes  STRIDE the frequency with which the grid should be output to the file=2000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=ffg FILE the file on which to write the grid=fesg STRIDE the frequency with which the grid should be output to the file=2000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=ffd FILE the file on which to write the grid=fesd STRIDE the frequency with which the grid should be output to the file=2000000

FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=2000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=molvol,coord.lessthan,b1.bias STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=colvar