**Project ID:** plumID:21.013

**Source:** ch4-diss/ni211/plumed.inp

**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 lengthsTIME=fsthe units of timeENERGY=kcal/molthe units of energyLOADLoads a library, possibly defining new actions. More detailsFILE=../../data/ReweightGeomFES.cppfile to be loadedDISTANCESCalculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More detailsGROUPA=110-113Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=109Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.010}calculate the maximum valueLABEL=a label for the action so that its output can be referenced in the input to other actionsd1DISTANCESCalculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More detailsGROUPA=109Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=1-108Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMIN={BETA=100.0}calculate the minimum valueLESS_THAN={RATIONAL R_0=2.5}calculate the number of variables less than a certain target valueLABEL=a label for the action so that its output can be referenced in the input to other actionsmetalcDISTANCESCalculate the distances between one or many pairs of atoms. You can then calculate functions of the distribution of More detailsGROUPA=110-113Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=1-108Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMIN={BETA=100.0}calculate the minimum valueLESS_THAN={RATIONAL R_0=2.0}calculate the number of variables less than a certain target valueLABEL=a label for the action so that its output can be referenced in the input to other actionsmetalhANGLESCalculate functions of the distribution of angles . More detailsGROUPA=109A group of central atoms about which angles should be calculatedGROUPB=110-113When used in conjunction with GROUPA this keyword instructs plumed to calculate all distinct angles involving one atom from GROUPA and two atoms from GROUPBBETWEEN={GAUSSIAN LOWER=0.5pi UPPER=0.7pi}calculate the number of values that are within a certain rangeSWITCH={RATIONAL D_0=1.50 R_0=0.25}A switching function that ensures that only angles between atoms that are within a certain fixed cutoff are calculatedLABEL=a label for the action so that its output can be referenced in the input to other actionsangCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=109this keyword is used for colvars such as the coordination numberSPECIESB=110-113this keyword is used for colvars such as the coordination numberR_0=1.75The r_0 parameter of the switching functionNN=12The n parameter of the switching functionMEANtake the mean of these variablesLABEL=a label for the action so that its output can be referenced in the input to other actionsd3COMBINECalculate 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.max,metalc.lessthan,metalh.lessthan,ang.betweenCOEFFICIENTS=0.901,0.177,-0.064,-0.390the 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 actionscvUPPER_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 actionsmetalc.min,cvAT=4.00,5.0the positions of the wallKAPPA=100,1the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionswall1UWALLSAdd ef UPPER_WALLS restraints on all the multicolvar values More detailsDATA=certain actions in plumed work by calculating a list of variables and summing over themd1AT=1.80the radius of the sphereKAPPA=500the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionswall2LOWER_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 actionsd3.meanAT=2.95the positions of the wallKAPPA=1000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionswall3METAD...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 actionscvSIGMA=0.05the widths of the Gaussian hillsHEIGHT=0.25the heights of the Gaussian hillsPACE=1000the frequency for hill additionBIASFACTOR=25use well tempered metadynamics and use this bias factorTEMP=500the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-3.0the lower bounds for the gridGRID_MAX=3.0the upper bounds for the gridGRID_BIN=1200the 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 factorLABEL=a label for the action so that its output can be referenced in the input to other actionsb1... METADREWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More detailsTEMP=500the system temperatureLABEL=a label for the action so that its output can be referenced in the input to other actionsbiasREWEIGHT_GEOMFESTEMP=500 ARG=This action is not part of PLUMED and was included by using a LOAD command More detailscvLABEL=gcvREWEIGHT_GEOMFESTEMP=500 ARG=This action is not part of PLUMED and was included by using a LOAD command More detailsd1.maxLABEL=g1REWEIGHT_GEOMFESTEMP=500 ARG=This action is not part of PLUMED and was included by using a LOAD command More detailsmetalc.lessthanLABEL=g2This action is not part of PLUMED and was included by using a LOAD command More detailsang.betweenLABEL=g3REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsTEMP=500the system temperatureARG=the biases that must be taken into account when reweightingwall1.bias,wall2.biasLABEL=a label for the action so that its output can be referenced in the input to other actionswbiasHISTOGRAM...Accumulate 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 actionscvGRID_MIN=-3.0the lower bounds for the gridGRID_MAX=3.0the upper bounds for the gridGRID_BIN=6000the 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 averagesbias,wbiasCLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=a label for the action so that its output can be referenced in the input to other actionshh... HISTOGRAMHISTOGRAM...Accumulate 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 actionscvGRID_MIN=-3.0the lower bounds for the gridGRID_MAX=3.0the upper bounds for the gridGRID_BIN=6000the 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 averagesbias,wbias,gcvCLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=a label for the action so that its output can be referenced in the input to other actionshhg... HISTOGRAMHISTOGRAM...Accumulate 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 actionsd1.maxGRID_MIN=1.0the lower bounds for the gridGRID_MAX=3.5the upper bounds for the gridGRID_BIN=2500the 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 averagesbias,wbias,g1CLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=a label for the action so that its output can be referenced in the input to other actionshh1... HISTOGRAMHISTOGRAM...Accumulate 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 actionsmetalc.lessthanGRID_MIN=0.0the lower bounds for the gridGRID_MAX=5.0the upper bounds for the gridGRID_BIN=2500the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density estimationbias,wbias,g2CLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=a label for the action so that its output can be referenced in the input to other actionshh2... HISTOGRAMHISTOGRAM...Accumulate 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 actionsang.betweenGRID_MIN=1.5the lower bounds for the gridGRID_MAX=4.5the upper bounds for the gridGRID_BIN=1500the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density estimationbias,wbias,g3CLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=a label for the action so that its output can be referenced in the input to other actionshh3... HISTOGRAMCONVERT_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 usehhTEMP=500.0the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsffCONVERT_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 usehhgTEMP=500.0the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsffgCONVERT_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 usehh1TEMP=500.0the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsff1Convert 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 usehh2TEMP=500.0the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsff2Convert 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 usehh3TEMP=500.0the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsff3DUMPGRIDOutput 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 outputffFILE=festhe file on which to write the gridSTRIDE=1000000the 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 outputffgFILE=fesgthe file on which to write the gridSTRIDE=1000000the 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 outputff1FILE=fes1the file on which to write the gridSTRIDE=1000000the 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 outputff2FILE=fes2the file on which to write the gridSTRIDE=1000000the 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 outputff3FILE=fes3the file on which to write the gridSTRIDE=1000000the 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=100000the 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 actionsd1.max,metalc.lessthan,metalh.lessthan,ang.between,d3.mean,cv,b1.bias,b1.rctSTRIDE=10000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities