Project ID: plumID:21.020
Source: dimer/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
UNITSThis command sets the internal units for the code. More detailsNATURALuse natural unitsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,2the pair of atom that we are calculating the distance betweenLABEL=dista label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=distthe arguments on which the bias is actingAT=7.0the positions of the wallKAPPA=1.0the force constant for the wallLABEL=wallsa label for the action so that its output can be referenced in the input to other actionsANN...Calculates the ANN-function. More detailsLABEL=fesfita label for the action so that its output can be referenced in the input to other actionsARG=distthe input for this action is the scalar output from one or more other actionsNUM_LAYERS=3number of layers of the neural networkNUM_NODES=1,12,1numbers of nodes in each layer of the neural networkACTIVATIONS=Tanh,Linearactivation functions for the neural networkWEIGHTS0=-1.10652425,-2.35390282,0.73520869,0.30508303,-1.91710758,-1.17080437,4.54476387,-1.55057519,-0.33438543,-0.51296629,-1.58933892,-0.66991935flattened 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,WEIGHTS1=1.12275159,-0.52419477,-1.68730803,0.54981566,-0.50883646,0.39913448,5.41323609,1.35671307,-0.83412662,0.09853493,2.40196946,-3.37362775flattened 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,BIASES0=0.92550763,-3.21503713,-2.65645714,-1.50841484,-3.84287814,0.98659592,-5.86437259,1.33560335,2.22786005,0.18571632,1.3609639,5.38428241bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2,BIASES1=1.14569644 ... ANNbias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2,CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=fesfit.node-0the input to this functionFUNC=-1.0*xthe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=wta label for the action so that its output can be referenced in the input to other actionsBIASVALUETakes the value of one variable and use it as a bias More detailsARG=wtthe input for this action is the scalar output from one or more other actionsLABEL=b1a label for the action so that its output can be referenced in the input to other actionsREWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsTEMP=1.5the system temperatureARG=b1.biasthe biases that must be taken into account when reweightingLABEL=biasa label for the action so that its output can be referenced in the input to other actionsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=distthe quantity that is being averagedGRID_MIN=0.0the lower bounds for the gridGRID_MAX=8.0the upper bounds for the gridGRID_BIN=1600the number of bins for the gridBANDWIDTH=0.1the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=hh ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hhthe histogram that you would like to convert into a free energy surface (old syntax)TEMP=1.5the temperature at which you are operatingLABEL=ffa label for the action so that its output can be referenced in the input to other actionsDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffthe grid you would like to print (can also use ARG for specifying what is being printed)FILE=festhe file on which to write the gridSTRIDE=1000000the frequency with which the grid should be output to the fileFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=10000the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARG=dist,b1.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=5000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities