Project ID: plumID:21.013
Source: ch4-diss/ni111/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
Click on the labels of the actions for more information on what each action computes
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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=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 one or many pairs of atoms. You can then calculate functions of the distribution of 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 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 one or many pairs of atoms. You can then calculate functions of the distribution of 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 less than a certain target valueLABEL=metalha label for the action so that its output can be referenced in the input to other actionsANGLESCalculate functions of the distribution of angles . 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}A switching function that ensures that only angles between atoms that are within a certain fixed cutoff are calculatedLABEL=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 functionMEANtake the mean of these variablesLABEL=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 for this action is the scalar output from one or more other actionsCOEFFICIENTS=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 input for this action is the scalar output from one or more other actionsAT=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 ef UPPER_WALLS restraints on all the multicolvar values More detailsDATA=d1certain actions in plumed work by calculating a list of variables and summing over themAT=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 input for this action is the scalar output from one or more other actionsAT=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 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 input for this action is the scalar output from one or more other actionsGRID_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=bias,wbiaslist of actions that calculates log weights that should be used to weight configurations when calculating averagesCLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=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 input for this action is the scalar output from one or more other actionsGRID_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=bias,wbias,gcvlist of actions that calculates log weights that should be used to weight configurations when calculating averagesCLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=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 input for this action is the scalar output from one or more other actionsGRID_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=bias,wbias,g1list of actions that calculates log weights that should be used to weight configurations when calculating averagesCLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=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 input for this action is the scalar output from one or more other actionsGRID_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 estimationLOGWEIGHTS=bias,wbias,g2list of actions that calculates log weights that should be used to weight configurations when calculating averagesCLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=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 input for this action is the scalar output from one or more other actionsGRID_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 estimationLOGWEIGHTS=bias,wbias,g3list of actions that calculates log weights that should be used to weight configurations when calculating averagesCLEAR=5000000the frequency with which to clear all the accumulated dataLABEL=hh3 ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=hhthe action that creates the input grid you would like to useTEMP=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, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=hhgthe action that creates the input grid you would like to useTEMP=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, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=hh1the action that creates the input grid you would like to useTEMP=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, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=hh2the action that creates the input grid you would like to useTEMP=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, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=hh3the action that creates the input grid you would like to useTEMP=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 action that creates the grid you would like to outputFILE=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 action that creates the grid you would like to outputFILE=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 action that creates the grid you would like to outputFILE=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 action that creates the grid you would like to outputFILE=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 action that creates the grid you would like to outputFILE=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