**Project ID:** plumID:21.009

**Source:** nvt-fes/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 lengthsLOADLoads a library, possibly defining new actions. More detailsFILE=../codes/ReweightGeomFES.cppfile to be loadedCOORDINATIONNUMBER...Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionscoordSPECIES=1-512this keyword is used for colvars such as coordination numberSWITCH={RATIONAL R_0=5.0 D_MAX=10.0}the switching function that it used in the construction of the contact matrixMORE_THAN={RATIONAL R_0=5.0 D_MAX=5.5}calculate the number of variables that are more than a certain target valueLOWMEM... COORDINATIONNUMBERthis flag does nothing and is present only to ensure back-compatibilityCOORDINATIONNUMBER...Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionscoord1SPECIES=1-512this keyword is used for colvars such as coordination numberR_0=5.0The r_0 parameter of the switching functionMORE_THAN={RATIONAL R_0=5.0 D_MAX=5.5}calculate the number of variables that are more than a certain target valueMOMENTS=2,3the list of moments that you would like to calculateLOWMEM... COORDINATIONNUMBERthis flag does nothing and is present only to ensure back-compatibilityUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingcoord.morethanAT=64the positions of the wallKAPPA=1.0the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionswallMETAD...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 actionscoord.morethanSIGMA=5000the widths of the Gaussian hillsADAPTIVE=DIFFuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeSIGMA_MIN=0.025the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=5.000the upper bounds for the sigmas (in CV units) when using adaptive hillsHEIGHT=0.5the heights of the Gaussian hillsPACE=10000the frequency for hill additionBIASFACTOR=15use well tempered metadynamics and use this bias factorTEMP=80.7the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=0.0the lower bounds for the gridGRID_MAX=140.0the upper bounds for the gridGRID_BIN=14000the 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=40the 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=80.7the system temperatureLABEL=a label for the action so that its output can be referenced in the input to other actionsbiasREWEIGHT_GEOMFESTEMP=80.7 ARG=This action is not part of PLUMED and was included by using a LOAD command More detailscoord.morethanLABEL=gd1HISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedcoord.morethanGRID_MIN=-0.2the lower bounds for the gridGRID_MAX=64the upper bounds for the gridGRID_BIN=6420the number of bins for the gridBANDWIDTH=0.1the bandwidths for kernel density esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesbiasCLEAR=40000000the frequency with whihc to clear the data that is being averagedLABEL=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 quantity that is being averagedcoord.morethanGRID_MIN=-0.2the lower bounds for the gridGRID_MAX=64the upper bounds for the gridGRID_BIN=6420the number of bins for the gridBANDWIDTH=0.1the bandwidths for kernel density esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesbias,gd1CLEAR=40000000the frequency with whihc to clear the data that is being averagedLABEL=a label for the action so that its output can be referenced in the input to other actionshhg... HISTOGRAMCONVERT_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)hhTEMP=80.7the 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 to a free energy surface. More detailsGRID=the histogram that you would like to convert into a free energy surface (old syntax)hhgTEMP=80.7the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsffgDUMPGRIDOutput 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)ffFILE=festhe file on which to write the gridSTRIDE=40000000the 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 grid you would like to print (can also use ARG for specifying what is being printed)ffgFILE=fesgthe file on which to write the gridSTRIDE=40000000the 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=200000the 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 actionscoord.morethan,coord1.morethan,coord1.moment-2,coord1.moment-3,b1.biasSTRIDE=2000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities