**Project ID:** plumID:22.008

**Source:** LJ-cluster/plumed.dat

**Originally used with PLUMED version:** 2.7

**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=0.0101805the units of timeENERGY=96.4853329the units of energyUNITSThis command sets the internal units for the code. More detailsNATURALuse natural unitsCOMCalculate the center of mass for a group of atoms. More detailsATOMS=1-7the list of atoms which are involved the virtual atom's definitionLABEL=a label for the action so that its output can be referenced in the input to other actionscomDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,the pair of atom that we are calculating the distance betweencomLABEL=a label for the action so that its output can be referenced in the input to other actionsd1UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd1AT=2.0the positions of the wallKAPPA=100the force constant for the wallDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,the pair of atom that we are calculating the distance betweencomLABEL=a label for the action so that its output can be referenced in the input to other actionsd2UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd2AT=2.0the positions of the wallKAPPA=100the force constant for the wallDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=3,the pair of atom that we are calculating the distance betweencomLABEL=a label for the action so that its output can be referenced in the input to other actionsd3UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd3AT=2.0the positions of the wallKAPPA=100the force constant for the wallDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=4,the pair of atom that we are calculating the distance betweencomLABEL=a label for the action so that its output can be referenced in the input to other actionsd4UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd4AT=2.0the positions of the wallKAPPA=100the force constant for the wallDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,the pair of atom that we are calculating the distance betweencomLABEL=a label for the action so that its output can be referenced in the input to other actionsd5UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd5AT=2.0the positions of the wallKAPPA=100the force constant for the wallDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=6,the pair of atom that we are calculating the distance betweencomLABEL=a label for the action so that its output can be referenced in the input to other actionsd6UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd6AT=2.0the positions of the wallKAPPA=100the force constant for the wallDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7,the pair of atom that we are calculating the distance betweencomLABEL=a label for the action so that its output can be referenced in the input to other actionsd7UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd7AT=2.0the positions of the wallKAPPA=100the force constant for the wallc1:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More detailsSPECIES=1-7this keyword is used for colvars such as coordination numberMOMENTS=2-3the list of moments that you would like to calculateSWITCH={RATIONAL R_0=1.5 NN=8 MM=16}the switching function that it used in the construction of the contact matrixMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=the input for this action is the scalar output from one or more other actionsc1HEIGHT=0.05the heights of the Gaussian hillsPACE=500the frequency for hill additionSIGMA=0.1,0.1the widths of the Gaussian hillsGRID_MIN=-1.5,-1.5the lower bounds for the gridGRID_MAX=2.5,2.5the upper bounds for the gridGRID_BIN=500,500the number of bins for the gridBIASFACTOR=5use well tempered metadynamics and use this bias factorFILE=HILLSa file in which the list of added hills is stored