Project ID: plumID:21.013
Source: ch4-diss/ni111-symm/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 multiple piars of atoms More detailsGROUPA=66-69Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=65Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMAX={BETA=0.010}calculate the maximum valueLABEL=d1a label for the action so that its output can be referenced in the input to other actionsDISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=65Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=1-64Calculate 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 that are less than a certain target valueLABEL=metalca label for the action so that its output can be referenced in the input to other actionsDISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=66-69Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=1-64Calculate 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 that are less than a certain target valueLABEL=metalha label for the action so that its output can be referenced in the input to other actionsANGLESCalculate an angle. More detailsGROUPA=65A group of central atoms about which angles should be calculatedGROUPB=66-69When 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}the switching function specifies that only those bonds that have a length that is less than a certain threshold are consideredLABEL=anga label for the action so that its output can be referenced in the input to other actionsCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=65this keyword is used for colvars such as the coordination numberSPECIESB=66-69this 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 functionMEANcalculate the mean of all the quantitiesLABEL=d3a label for the action so that its output can be referenced in the input to other actionsCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1.max,metalc.lessthan,metalh.lessthan,ang.betweenthe input to this functionCOEFFICIENTS=0.952,0.225,-0.091,-0.187the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=cva label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=metalc.min,cvthe arguments on which the bias is actingAT=4.00,5.0the positions of the wallKAPPA=100,1the force constant for the wallLABEL=wall1a label for the action so that its output can be referenced in the input to other actionsUWALLSAdd lower walls to a vector of quantities More detailsDATA=d1the values you want to restrainAT=1.80the radius of the sphereKAPPA=250the force constant for the wallLABEL=wall2a label for the action so that its output can be referenced in the input to other actionsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d3.meanthe arguments on which the bias is actingAT=2.95the positions of the wallKAPPA=1000the force constant for the wallLABEL=wall3a label for the action so that its output can be referenced in the input to other actionsCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=66-69this keyword is used for colvars such as the coordination numberSPECIESB=65this keyword is used for colvars such as the coordination numberD_0=0.85The d_0 parameter of the switching functionR_0=0.25The r_0 parameter of the switching functionNN=1The n parameter of the switching functionMEANcalculate the mean of all the quantitiesMOMENTS=2the list of moments that you would like to calculateLABEL=nma label for the action so that its output can be referenced in the input to other actionsEXTERNALCalculate a restraint that is defined on a grid that is read during start up More detailsARG=nm.meanthe input for this action is the scalar output from one or more other actionsFILE=extbiasthe name of the file containing the external potentialLABEL=externala label for the action so that its output can be referenced in the input to other actionsMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=cvthe input for this action is the scalar output from one or more other actionsSIGMA=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=b1 ... METADa label for the action so that its output can be referenced in the input to other actionsREWEIGHT_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=biasa label for the action so that its output can be referenced in the input to other actionsREWEIGHT_GEOMFESTEMP=500 ARG=cv LABEL=gcvThis action is not part of PLUMED and was included by using a LOAD command More detailsREWEIGHT_GEOMFESTEMP=500 ARG=d1.max LABEL=g1This action is not part of PLUMED and was included by using a LOAD command More detailsREWEIGHT_GEOMFESTEMP=500 ARG=metalc.lessthan LABEL=g2This action is not part of PLUMED and was included by using a LOAD command More detailsREWEIGHT_GEOMFESTEMP=500 ARG=ang.between LABEL=g3This action is not part of PLUMED and was included by using a LOAD command More detailsREWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsTEMP=500the system temperatureARG=wall1.bias,wall2.biasthe biases that must be taken into account when reweightingLABEL=wbiasa label for the action so that its output can be referenced in the input to other actionsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=cvthe quantity that is being averagedGRID_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 esimtationLOGWEIGHTS=bias,wbiasthe logarithm of the quantity to use as the weights when calculating averagesCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=hh ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=cvthe quantity that is being averagedGRID_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 esimtationLOGWEIGHTS=bias,wbias,gcvthe logarithm of the quantity to use as the weights when calculating averagesCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=hhg ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=d1.maxthe quantity that is being averagedGRID_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 esimtationLOGWEIGHTS=bias,wbias,g1the logarithm of the quantity to use as the weights when calculating averagesCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=hh1 ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=metalc.lessthanthe quantity that is being averagedGRID_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 esimtationLOGWEIGHTS=bias,wbias,g2the logarithm of the quantity to use as the weights when calculating averagesCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=hh2 ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=ang.betweenthe quantity that is being averagedGRID_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 esimtationLOGWEIGHTS=bias,wbias,g3the logarithm of the quantity to use as the weights when calculating averagesCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=hh3 ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hhthe histogram that you would like to convert into a free energy surface (old syntax)TEMP=500.0the temperature at which you are operatingLABEL=ffa label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hhgthe histogram that you would like to convert into a free energy surface (old syntax)TEMP=500.0the temperature at which you are operatingLABEL=ffga label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hh1the histogram that you would like to convert into a free energy surface (old syntax)TEMP=500.0the temperature at which you are operatingLABEL=ff1a label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hh2the histogram that you would like to convert into a free energy surface (old syntax)TEMP=500.0the temperature at which you are operatingLABEL=ff2a label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hh3the histogram that you would like to convert into a free energy surface (old syntax)TEMP=500.0the temperature at which you are operatingLABEL=ff3a label for the action so that its output can be referenced in the input to other actionsDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffthe grid you would like to print (can also use ARG for specifying what is being printed)FILE=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=ffgthe grid you would like to print (can also use ARG for specifying what is being printed)FILE=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=ff1the grid you would like to print (can also use ARG for specifying what is being printed)FILE=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=ff2the grid you would like to print (can also use ARG for specifying what is being printed)FILE=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=ff3the grid you would like to print (can also use ARG for specifying what is being printed)FILE=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=d1.max,metalc.lessthan,metalh.lessthan,ang.between,d3.mean,cv,b1.bias,b1.rctthe input for this action is the scalar output from one or more other actionsSTRIDE=10000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities