**Project ID:** plumID:21.032

**Source:** plumed_fes_1_2.dat

**Originally used with PLUMED version:** 2.6

**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 lengthsENERGY=kcal/molthe units of energyWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-781the atoms that make up a molecule that you wish to alignSTRIDE=1the frequency with which molecules are reassembledmetad:READRead quantities from a colvar file. More detailsFILE=COLVAR_REWEIGHTthe name of the file from which to read these quantitiesIGNORE_TIMEignore the time in the colvar fileVALUES=the values to read from the filemetad.biasweights1:REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More detailsTEMP=300the system temperatureARG=the biases that must be taken into account when reweightingmetad.biasGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=67,88,243,292the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn69GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=152,88,324,173the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn68GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=211,292,359,173the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn67ATOMS=465,455,628,434the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn66ATOMS=512,554,465,761the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn65ATOMS=599,424,434,554the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn64ATOMS=751,761,730,628the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn63zn:ATOMS=775-781the numerical indexes for the set of atoms in the groupCys:ATOMS=67,88,243,292,152,324,173,211,359,465,455,628,434,512,554,761,599,424,751,730the numerical indexes for the set of atoms in the groupzn69:COORDINATIONCalculate coordination numbers. More detailsGROUPA=781First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn69SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}This keyword is used if you want to employ an alternative to the continuous switching function defined abovezn68:COORDINATIONCalculate coordination numbers. More detailsGROUPA=780First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn68SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}This keyword is used if you want to employ an alternative to the continuous switching function defined abovezn67:COORDINATIONCalculate coordination numbers. More detailsGROUPA=779First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn67SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}This keyword is used if you want to employ an alternative to the continuous switching function defined abovezn66:COORDINATIONCalculate coordination numbers. More detailsGROUPA=778First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn66zn65:COORDINATIONCalculate coordination numbers. More detailsGROUPA=777First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn65zn64:COORDINATIONCalculate coordination numbers. More detailsGROUPA=776First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn64zn63:COORDINATIONCalculate coordination numbers. More detailsGROUPA=775First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn63zn69_filterbbb:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=781this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn69SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixzn68_filterbbb:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=780this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn68SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixzn67_filterbbb:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=779this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn67SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixzn66_filterbbb:SPECIESA=778this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn66SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixzn65_filterbbb:SPECIESA=777this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn65SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixzn64_filterbbb:SPECIESA=776this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn64SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixzn63_filterbbb:SPECIESA=775this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn63SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixzn69_filter:SPECIESA=781this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn69SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesMORE_THAN={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}calculate the number of variables that are more than a certain target valuezn68_filter:SPECIESA=780this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn68SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesMORE_THAN={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}calculate the number of variables that are more than a certain target valuezn67_filter:SPECIESA=779this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn67SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesMORE_THAN={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}calculate the number of variables that are more than a certain target valuezn66_filter:SPECIESA=778this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn66SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesMORE_THAN={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}calculate the number of variables that are more than a certain target valuezn65_filter:SPECIESA=777this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn65SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesMORE_THAN={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}calculate the number of variables that are more than a certain target valuezn64_filter:SPECIESA=776this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn64SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesMORE_THAN={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}calculate the number of variables that are more than a certain target valuezn63_filter:SPECIESA=775this keyword is used for colvars such as the coordination numberSPECIESB=this keyword is used for colvars such as the coordination numbercomCysZn63SWITCH={RATIONAL R_0=2.9 D_MAX=5 NN=12 MM=24}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesMORE_THAN={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}calculate the number of variables that are more than a certain target valueMFILTER_MOREBasically equivalent to MORE_THAN. More detailsDATA=the vector you wish to transformzn69_filterbbbSWITCH={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}the switching function that transformLOWMEMthis flag does nothing and is present only to ensure back-compatibilityLABEL=a label for the action so that its output can be referenced in the input to other actionsd69HIGHESTthis flag allows you to recover the highest of these variablesMFILTER_MOREBasically equivalent to MORE_THAN. More detailsDATA=the vector you wish to transformzn68_filterbbbSWITCH={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}the switching function that transformLOWMEMthis flag does nothing and is present only to ensure back-compatibilityLABEL=a label for the action so that its output can be referenced in the input to other actionsd68HIGHESTthis flag allows you to recover the highest of these variablesMFILTER_MOREBasically equivalent to MORE_THAN. More detailsDATA=the vector you wish to transformzn67_filterbbbSWITCH={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}the switching function that transformLOWMEMthis flag does nothing and is present only to ensure back-compatibilityLABEL=a label for the action so that its output can be referenced in the input to other actionsd67HIGHESTthis flag allows you to recover the highest of these variablesMFILTER_MOREBasically equivalent to MORE_THAN. More detailsDATA=the vector you wish to transformzn66_filterbbbSWITCH={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}the switching function that transformLOWMEMthis flag does nothing and is present only to ensure back-compatibilityLABEL=a label for the action so that its output can be referenced in the input to other actionsd66HIGHESTthis flag allows you to recover the highest of these variablesMFILTER_MOREBasically equivalent to MORE_THAN. More detailsDATA=the vector you wish to transformzn65_filterbbbSWITCH={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}the switching function that transformLOWMEMthis flag does nothing and is present only to ensure back-compatibilityLABEL=a label for the action so that its output can be referenced in the input to other actionsd65HIGHESTthis flag allows you to recover the highest of these variablesMFILTER_MOREBasically equivalent to MORE_THAN. More detailsDATA=the vector you wish to transformzn64_filterbbbSWITCH={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}the switching function that transformLOWMEMthis flag does nothing and is present only to ensure back-compatibilityLABEL=a label for the action so that its output can be referenced in the input to other actionsd64HIGHESTthis flag allows you to recover the highest of these variablesMFILTER_MOREBasically equivalent to MORE_THAN. More detailsDATA=the vector you wish to transformzn63_filterbbbSWITCH={RATIONAL R_0=3.2 D_MAX=5 NN=12 MM=24}the switching function that transformLOWMEMthis flag does nothing and is present only to ensure back-compatibilityLABEL=a label for the action so that its output can be referenced in the input to other actionsd63HIGHESTthis flag allows you to recover the highest of these variablesCyss2:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functiond69.highest,d68.highest,d67.highest,d66.highest,d65.highest,d64.highest,d63.highestPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionm:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functionzn69_filter.morethan,zn68_filter.morethan,zn67_filter.morethan,zn66_filter.morethan,zn65_filter.morethan,zn64_filter.morethan,zn63_filter.morethanPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionDRMSDCalculate the distance RMSD with respect to a reference structure. More detailsREFERENCE=reference.pdba file in pdb format containing the reference structure and the atoms involved in the CVLOWER_CUTOFF=0.1only pairs of atoms further than LOWER_CUTOFF are considered in the calculationUPPER_CUTOFF=8only pairs of atoms closer than UPPER_CUTOFF are considered in the calculationLABEL=a label for the action so that its output can be referenced in the input to other actionsDRMSDHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedCyss2,mGRID_MIN=0,0the lower bounds for the gridGRID_MAX=30,10the upper bounds for the gridBANDWIDTH=0.4,0.4the bandwidths for kernel density esimtationGRID_BIN=300,300the number of bins for the gridLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesweights1LABEL=a label for the action so that its output can be referenced in the input to other actionshB6NORMALIZATION=false ... HISTOGRAMThis controls how the data is normalized it can be set equal to true, false or ndataHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedm,DRMSDGRID_MIN=0,0the lower bounds for the gridGRID_MAX=9,12the upper bounds for the gridGRID_BIN=300,300the number of bins for the gridBANDWIDTH=0.5,0.5the bandwidths for kernel density esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesweights1LABEL=a label for the action so that its output can be referenced in the input to other actionshB5NORMALIZATION=false ... HISTOGRAMThis controls how the data is normalized it can be set equal to true, false or ndatafes6:CONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=the histogram that you would like to convert into a free energy surface (old syntax)hB6TEMP=300the temperature at which you are operatingfes5:CONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=the histogram that you would like to convert into a free energy surface (old syntax)hB5TEMP=300the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the grid you would like to print (can also use ARG for specifying what is being printed)hB6FILE=histo6.datthe file on which to write the gridFMT=%8.4fthe format that should be used to output real numbersDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the grid you would like to print (can also use ARG for specifying what is being printed)hB5FILE=histo5.datthe file on which to write the gridFMT=%8.4fthe format that should be used to output real numbersDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the grid you would like to print (can also use ARG for specifying what is being printed)fes6FILE=the file on which to write the gridfes6.datFMT=%8.4fthe format that should be used to output real numbersDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the grid you would like to print (can also use ARG for specifying what is being printed)fes5FILE=the file on which to write the gridfes5.datFMT=%8.4fthe format that should be used to output real numbers