**Project ID:** plumID:19.054

**Source:** plumed.dat

**Originally used with PLUMED version:** 2.3

**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=0.001 #Amstroeng, hartree, fsthe units of timeene:ENERGYCalculate the total potential energy of the simulation box. More detailsd1:DISTANCECalculate 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 distancesd5:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,6the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesc1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functiond1,d5COEFFICIENTS=0.500,-0.500the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionh1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,3the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesh2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,4the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesh3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,5the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd1AT=+4.0the positions of the wallKAPPA=150.0the force constant for the wallEXP=2the powers for the wallsLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_1UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd5AT=+4.0the positions of the wallKAPPA=150.0the force constant for the wallEXP=2the powers for the wallsLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall_2LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingh1AT=+1.7the positions of the wallKAPPA=150.0the force constant for the wallEXP=2the powers for the wallsLABEL=a label for the action so that its output can be referenced in the input to other actionslwall_1LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingh2AT=+1.7the positions of the wallKAPPA=150.0the force constant for the wallEXP=2the powers for the wallsLABEL=a label for the action so that its output can be referenced in the input to other actionslwall_2LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingh3AT=+1.7the positions of the wallKAPPA=150.0the force constant for the wallEXP=2the powers for the wallsLABEL=a label for the action so that its output can be referenced in the input to other actionslwall_3METAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsmetadARG=the input for this action is the scalar output from one or more other actionsc1PACE=50the frequency for hill additionHEIGHT=2.0the heights of the Gaussian hillsSIGMA=0.1the widths of the Gaussian hillsFILE=HILLSa file in which the list of added hills is storedBIASFACTOR=50use well tempered metadynamics and use this bias factorTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsCALC_RCTcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]GRID_MIN=-4the lower bounds for the gridGRID_MAX=+4the upper bounds for the gridGRID_BIN=1000 ... METADthe number of bins for the gridPrint quantities to a file. More detailsSTRIDE=1the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesARG=the input for this action is the scalar output from one or more other actionsd1,d5,c1,metad.*,eneFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1the frequency with which all the open files should be flushed