Project ID: plumID:21.020
Source: sn2/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 detailsLENGTH=Athe units of lengthsTIME=fsthe units of timeDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,2the pair of atom that we are calculating the distance betweenLABEL=d1a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,6the pair of atom that we are calculating the distance betweenLABEL=d2a label for the action so that its output can be referenced in the input to other actionsCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1,d2the input to this functionCOEFFICIENTS=0.707,-0.707the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=cva 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=d1,d2the arguments on which the bias is actingAT=5.0,5.0the positions of the wallKAPPA=100.0,100.0the force constant for the wallLABEL=constraina 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=cvthe 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=3.56561455,-6.71040355,5.25044716,7.7231881,-7.91816755,-5.97251384,3.84144036,-4.82860899,-7.53180985,6.26159315,-4.12440194,4.40081403flattened 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=7.89933249,5.06936118,3.93503597,3.88241017,-3.86538677,8.43184926,3.47606736,-3.72495959,6.24588806,3.35531128,4.67826819,-3.95806807flattened 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=-3.96371368,4.17326354,2.60848734,1.27662432,-2.49483138,1.35277058,2.71088811,-2.84712335,3.2062986,2.70329581,-4.1852847,5.51867405bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2,BIASES1=2.44193157 ... 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=300the 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=cvthe quantity that is being averagedGRID_MIN=-2.0the lower bounds for the gridGRID_MAX=2.0the upper bounds for the gridGRID_BIN=4000the number of bins for the gridBANDWIDTH=0.05the 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=300.0the 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=20000the 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=2000the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARG=cv,b1.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=200the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities