PLUMED-NEST-TEST-SITE

Project ID: plumID:21.020
Source: hbr/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

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs

The UNITS action with label  calculates somethingd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,11 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,1  NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,2  NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,2  NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,1  NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2   NOPBC ignore the periodic boundary conditions when calculating distances

The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2,d3,d4,d5,d6 ATthe positions of the wall=3.0,3.0,3.0,3.0,3.0,3.0 KAPPAthe force constant for the wall=100,100,100,100,100,100

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 potentialcv: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d5,d6 COEFFICIENTS the coefficients of the arguments in your function=0.661,-0.656,-0.328,0.011,-0.021,0.157 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO


The COMBINE action with label cv calculates the following quantities:
 Quantity   
 Description  
cv.value
a linear compbinationANNCalculates 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=cv
  NUM_LAYERSnumber of layers of the neural network=3
  NUM_NODESnumbers of nodes in each layer of the neural network=1,48,1
  ACTIVATIONSactivation functions for the neural network=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, =7.02603134,-7.10656245,6.87468804,6.44175163,-8.05901739,-9.92301921,8.70412179,5.24445234,-7.15034183,-4.89640601,5.23411097,-6.16335667,-5.80727531,6.09854222,9.03723364,-6.19909808,4.87341508,5.4844505,5.17560729,5.05697771,5.93438394,-5.71471957,-4.80556544,7.25557632,9.47419942,-4.59945602,6.16870363,8.73579702,-6.5963175,-3.4826426,6.87015659,4.32398507,-5.7119825,-3.62043586,5.52290261,-5.41269008,6.43750182,-4.61871456,6.61789092,4.69954468,8.29040765,-10.11716514,7.04612104,-5.44254231,4.57136333,-9.15486747,-4.94113593,6.71545542
  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, =-3.07574091,-9.89746009,-3.15299416,-3.24530278,-9.57739595,2.77604802,-3.4314115,-1.92436265,3.29843627,1.49236991,-2.84250541,-9.95369648,-9.3124519,-2.90663917,9.80867586,2.96358348,-1.62958348,-2.53223939,-2.79371778,-1.62894969,-3.27305257,2.6427191,1.48710888,-3.2627269,-3.67837903,-5.63907048,-2.36960156,-3.95901324,3.13753686,-9.23112732,-3.31650521,-0.72276839,2.75064713,-10.09041104,-2.92406711,2.72257186,-3.08722293,-5.56477804,-2.42215226,6.64587078,-3.33581553,3.29791456,-3.39129346,-9.53846615,-0.94354542,3.45900422,1.88059984,-2.90541763
  BIASES0bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, =0.1902818,-4.10551933,0.22589334,-0.07582383,-3.50552854,-2.19018425,1.90013798,-1.35713566,-1.4730146,0.93418965,-0.69205605,-3.8355124,-6.29137461,-1.62394629,3.20821655,1.79014226,-0.93558303,-1.48051528,-0.78992735,-1.17037756,-0.24011175,2.67836642,0.87249589,0.15014032,2.08530087,-3.58209149,-1.6350707,1.90793108,0.03897141,3.48234302,0.22687527,-0.68752415,2.67617444,3.60703902,-2.49713368,3.77533027,0.41214063,-3.60686151,-4.82613345,3.70799175,1.79634271,-2.2350788,0.0519425,-4.51020721,-0.75313181,-2.009491,1.03992807,-0.01423335
  BIASES1bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, =-10.3903018
... 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-100) 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=300 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 biasHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=cv
  GRID_MIN the lower bounds for the grid=-2.0
  GRID_MAX the upper bounds for the grid=2.0
  GRID_BINthe number of bins for the grid=4000
  BANDWIDTHthe bandwidths for kernel density esimtation=0.02
  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=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 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=300.0 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 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=20000

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=d1,d2,d3,d4,d5,d6,cv,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