**Project ID:** plumID:20.018

**Source:** da-wt/plumed.inp

**Originally used with PLUMED version:** 2.6-mod

**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 timeENERGY=kcal/molthe units of energyLOADLoads a library, possibly defining new actions. More detailsFILE=../src/bias/ReweightGeomFES.cppfile to be loadedDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,2the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd1DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,3the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd2DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=3,4the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd3DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=4,5the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd4DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,6the pair of atom that we are calculating the distance betweenLABEl=a label for the action so that its output can be referenced in the input to other actionsd5DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,6the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd6COORDINATIONCalculate coordination numbers. More detailsGROUPA=4First list of atomsGROUPB=5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=1.0The d_0 parameter of the switching functionR_0=1.0The r_0 parameter of the switching functionNN=1The n parameter of the switching functionLABEL=a label for the action so that its output can be referenced in the input to other actionscn1COORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=1.0The d_0 parameter of the switching functionR_0=1.0The r_0 parameter of the switching functionNN=1The n parameter of the switching functionLABEL=a label for the action so that its output can be referenced in the input to other actionscn2DENSITYCalculate functions of the density of atoms as a function of the box. This allows one to calculate More detailsSPECIES=5,6this keyword is used for colvars such as coordination numberLABEL=a label for the action so that its output can be referenced in the input to other actionsethyleneDENSITYCalculate functions of the density of atoms as a function of the box. This allows one to calculate More detailsSPECIES=1-4this keyword is used for colvars such as coordination numberLABEL=a label for the action so that its output can be referenced in the input to other actionsdieneCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1-4the 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 actionsmol1CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=5-6the 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 actionsmol2CONTACT_MATRIX...Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsATOMS=The list of atoms for which you would like to calculate the contact matrixethylene,dieneSWITCH11={RATIONAL D_0=0.0 R_0=2.65}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveSWITCH12={RATIONAL D_0=0.0 R_0=2.65}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveSWITCH22={RATIONAL D_0=0.0 R_0=2.65}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveLABEL=a label for the action so that its output can be referenced in the input to other actionsmat1... CONTACT_MATRIXCONTACT_MATRIX...Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More detailsATOMS=The list of atoms for which you would like to calculate the contact matrixethylene,dieneSWITCH11={RATIONAL D_0=0.0 R_0=2.12 NN=24}SWITCH12={RATIONAL D_0=0.0 R_0=2.12 NN=24}SWITCH22={RATIONAL D_0=0.0 R_0=2.12 NN=24}LABEL=a label for the action so that its output can be referenced in the input to other actionsmat2... CONTACT_MATRIXCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=this keyword is used for colvars such as the coordination numberethyleneSPECIESB=this keyword is used for colvars such as the coordination numberdieneMEANtake the mean of these variablesSWITCH={GAUSSIAN D_0=1.8 R_0=0.3}LABEL=a label for the action so that its output can be referenced in the input to other actionscnSPRINTCalculate SPRINT topological variables from an adjacency matrix. More detailsMATRIX=the action that calculates the adjacency matrix vessel we would like to analyzemat1LABEL=a label for the action so that its output can be referenced in the input to other actionsss1SPRINTCalculate SPRINT topological variables from an adjacency matrix. More detailsMATRIX=the action that calculates the adjacency matrix vessel we would like to analyzemat2LABEL=a label for the action so that its output can be referenced in the input to other actionsss2DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenmol1,mol2LABEL=a label for the action so that its output can be referenced in the input to other actionsdistCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d6COEFFICIENTS=-0.05,0.21,-0.08,0.69,0.69the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=a label for the action so that its output can be referenced in the input to other actionshldaCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input for this action is the scalar output from one or more other actionscn1,cn2COEFFICIENTS=0.5,0.5the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=a label for the action so that its output can be referenced in the input to other actionssimpleCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input for this action is the scalar output from one or more other actionsss1.coord-0,ss1.coord-1COEFFICIENTS=0.5,0.5the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=a label for the action so that its output can be referenced in the input to other actionssprnt1COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input for this action is the scalar output from one or more other actionsss2.coord-0,ss2.coord-1COEFFICIENTS=0.5,0.5the coefficients of the arguments in your functionif the output of your function is periodic then you should specify the periodicity of the functionLABEL=a label for the action so that its output can be referenced in the input to other actionssprnt2UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsd4,d6AT=5.0,5.0the positions of the wallKAPPA=50,50the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionswallsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdist,sprnt1,sprnt2,cn.mean,simpleAT=0,0,0,0,0the positions of the wallKAPPA=50,50,50,50,50the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsfakeMETAD...Used 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 actionshldaSIGMA=0.15the widths of the Gaussian hillsHEIGHT=1.0the heights of the Gaussian hillsPACE=1000the frequency for hill additionBIASFACTOR=25use well tempered metadynamics and use this bias factorTEMP=600the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=1.0the lower bounds for the gridGRID_MAX=9.0the upper bounds for the gridGRID_BIN=1600the 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=1the update stride for calculating the $c(t)$ reweighting factorRESTART=YESallows per-action setting of restart (YES/NO/AUTO)LABEL=a label for the action so that its output can be referenced in the input to other actionsb1... METADREWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsARG=the biases that must be taken into account when reweightingb1.biasTEMP=600the system temperatureLABEL=a label for the action so that its output can be referenced in the input to other actionsbiasREWEIGHT_GEOMFESARG=This action is not part of PLUMED and was included by using a LOAD command More detailsd4TEMP=600 LABEL=gd4REWEIGHT_GEOMFESARG=This action is not part of PLUMED and was included by using a LOAD command More detailshldaTEMP=600 LABEL=ghldaREWEIGHT_GEOMFESARG=This action is not part of PLUMED and was included by using a LOAD command More detailssprnt1TEMP=600 LABEL=gsprnt1This action is not part of PLUMED and was included by using a LOAD command More detailssprnt2TEMP=600 LABEL=gsprnt2This action is not part of PLUMED and was included by using a LOAD command More detailscn.meanTEMP=600 LABEL=gcnThis action is not part of PLUMED and was included by using a LOAD command More detailssimpleTEMP=600 LABEL=gsimpleThis action is not part of PLUMED and was included by using a LOAD command More detailsd4,d6TEMP=600 LABEL=g2dHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionsd4GRID_MIN=1.0the lower bounds for the gridGRID_MAX=6.0the upper bounds for the gridGRID_BIN=2000the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density estimationLOGWEIGHTS=list of actions that calculates log weights that should be used to weight configurations when calculating averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshd4HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionshldaGRID_MIN=1.0the lower bounds for the gridGRID_MAX=9.0the upper bounds for the gridGRID_BIN=4000the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density estimationLOGWEIGHTS=list of actions that calculates log weights that should be used to weight configurations when calculating averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshhldaHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionssprnt1GRID_MIN=0.0the lower bounds for the gridGRID_MAX=4.0the upper bounds for the gridGRID_BIN=2000the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density estimationLOGWEIGHTS=list of actions that calculates log weights that should be used to weight configurations when calculating averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshsprnt1HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionssprnt2GRID_MIN=-0.1the lower bounds for the gridGRID_MAX=2.4the upper bounds for the gridGRID_BIN=2500the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density estimationbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshsprnt2HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionssimpleGRID_MIN=0.1the lower bounds for the gridGRID_MAX=0.8the upper bounds for the gridGRID_BIN=3500the number of bins for the gridBANDWIDTH=0.001the bandwidths for kernel density estimationbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshsimpleHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionsd4,d6GRID_MIN=1.0,1.0the lower bounds for the gridGRID_MAX=2.0,2.0the upper bounds for the gridGRID_BIN=100,100the number of bins for the gridBANDWIDTH=0.04,0.04the bandwidths for kernel density estimationbiasLABEL=a label for the action so that its output can be referenced in the input to other actionsh2dbHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionsd4,d6GRID_MIN=2.0,2.0the lower bounds for the gridGRID_MAX=6.0,6.0the upper bounds for the gridGRID_BIN=80,80the number of bins for the gridBANDWIDTH=0.20,0.20the bandwidths for kernel density estimationbiasLABEL=a label for the action so that its output can be referenced in the input to other actionsh2ddHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionsd4,d6GRID_MIN=2.0,2.0the lower bounds for the gridGRID_MAX=2.2,2.2the upper bounds for the gridGRID_BIN=100,100the number of bins for the gridBANDWIDTH=0.02,0.02the bandwidths for kernel density estimationbiasLABEL=a label for the action so that its output can be referenced in the input to other actionsh2dHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionsd4GRID_MIN=1.0the lower bounds for the gridGRID_MAX=6.0the upper bounds for the gridGRID_BIN=2000the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density estimationbias,gd4LABEL=a label for the action so that its output can be referenced in the input to other actionshd4gHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionshldaGRID_MIN=1.0the lower bounds for the gridGRID_MAX=9.0the upper bounds for the gridGRID_BIN=4000the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density estimationbias,ghldaLABEL=a label for the action so that its output can be referenced in the input to other actionshhldagHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionssprnt1GRID_MIN=0.0the lower bounds for the gridGRID_MAX=4.0the upper bounds for the gridGRID_BIN=2000the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density estimationbias,gsprnt1LABEL=a label for the action so that its output can be referenced in the input to other actionshsprnt1gHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionssprnt2GRID_MIN=-0.1the lower bounds for the gridGRID_MAX=2.4the upper bounds for the gridGRID_BIN=2500the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density estimationbias,gsprnt2LABEL=a label for the action so that its output can be referenced in the input to other actionshsprnt2gHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionssimpleGRID_MIN=0.1the lower bounds for the gridGRID_MAX=0.8the upper bounds for the gridGRID_BIN=3500the number of bins for the gridBANDWIDTH=0.001the bandwidths for kernel density estimationbias,gsimpleLABEL=a label for the action so that its output can be referenced in the input to other actionshsimplegHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionsd4,d6GRID_MIN=2.0,2.0the lower bounds for the gridGRID_MAX=2.2,2.2the upper bounds for the gridGRID_BIN=100,100the number of bins for the gridBANDWIDTH=0.02,0.02the bandwidths for kernel density estimationbias,g2dLABEL=a label for the action so that its output can be referenced in the input to other actionsh2dgCONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehd4TEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfd4CONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehhldaTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfhldaCONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehsprnt1TEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfsprnt1Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehsprnt2TEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfsprnt2Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehsimpleTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfsimpleConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to useh2dbTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsf2dbConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to useh2ddTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsf2ddConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to useh2dTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsf2dConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehd4gTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfd4gConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehhldagTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfhldagConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehsprnt1gTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfsprnt1gConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehsprnt2gTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfsprnt2gConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehsimplegTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfsimplegConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to useh2dgTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsf2dgDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfd4FILE=fesd4the file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfhldaFILE=feshldathe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfsprnt1FILE=fessprnt1the file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfsprnt2FILE=fessprnt2the file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfsimpleFILE=fessimplethe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputf2dbFILE=fes2dbthe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputf2ddFILE=fes2ddthe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputf2dFILE=fes2dthe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfd4gFILE=fesd4gthe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfhldagFILE=feshldagthe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfsprnt1gFILE=fessprnt1gthe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfsprnt2gFILE=fessprnt2gthe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputfsimplegFILE=fessimplegthe file on which to write the gridSTRIDE=5000000the frequency with which the grid should be output to the fileDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputf2dgFILE=fes2dgthe file on which to write the gridSTRIDE=5000000the 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=the input for this action is the scalar output from one or more other actionsd4,d6,hlda,dist,cn.mean,sprnt1,sprnt2,b1.bias,b1.rctSTRIDE=200the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities