Project ID: plumID:21.020
Source: hbr/metad/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 functionMETADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More detailsARG=cvthe input for this action is the scalar output from one or more other actionsPACE=200the frequency for hill additionHEIGHT=5.0the heights of the Gaussian hillsSIGMA=0.2the widths of the Gaussian hillsTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsBIASFACTOR=50use well tempered metadynamics and use this bias factorGRID_MIN=-3.0the lower bounds for the gridGRID_MAX=2.0the upper bounds for the gridGRID_BIN=5000the number of bins for the gridCALC_RCTcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]RCT_USTRIDE=10the update stride for calculating the c(t) reweighting factorLABEL=b1a label for the action so that its output can be referenced in the input to other actionsCONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More detailsVALUE=100.0the single number that you would like to storeLABEL=cnsta 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=cnstthe input for this action is the scalar output from one or more other actionsLABEL=dummya label for the action so that its output can be referenced in the input to other actionsREWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. This action has hidden defaults. More detailsTEMP=300the system temperatureLABEL=biasa 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 detailsARG=dummy.biasthe biases that must be taken into account when reweightingTEMP=300the system temperatureLABEL=duma 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. This action is a shortcut and it has hidden defaults. 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 esimtationCLEAR=200000the frequency with whihc to clear the data that is being averagedLOGWEIGHTS=bias,dumthe 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. This action is a shortcut. 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=200000the 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