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
UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsTIME=fsthe units of time
d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,11the pair of atom that we are calculating the distance betweenNOPBCd2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=11,1the pair of atom that we are calculating the distance betweenNOPBCd3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,2the pair of atom that we are calculating the distance betweenNOPBCd4:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=11,2the pair of atom that we are calculating the distance betweenNOPBCd5:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,1the pair of atom that we are calculating the distance betweenNOPBCd6:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,2the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distances
uwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d1,d2,d3,d4,d5,d6the arguments on which the bias is actingAT=3.0,3.0,3.0,3.0,3.0,3.0the positions of the wallKAPPA=100,100,100,100,100,100the force constant for the wall
cv:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1,d2,d3,d4,d5,d6the input to this functionCOEFFICIENTS=0.661,-0.656,-0.328,0.011,-0.021,0.157the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionANN...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=1,48,1numbers of nodes in each layer of the neural networkACTIVATIONS=Tanh,Linearactivation functions for the neural networkWEIGHTS0=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,-4.94113593,6.71545542flattened 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=-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,-2.90541763flattened 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=0.1902818,-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,-0.01423335bias array for each layer of the neural network, BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2,BIASES1=-10.3903018 ... 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*(x-100the 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=0.02the 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=d1,d2,d3,d4,d5,d6,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