Project ID: plumID:19.080
Source: h3/explicit/plumed.inp
Originally used with PLUMED version: 2.4.1
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 energyDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,2the pair of atom that we are calculating the distance betweenLABEL=d1a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,3the pair of atom that we are calculating the distance betweenLABEL=d2a label for the action so that its output can be referenced in the input to other actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,3the pair of atom that we are calculating the distance betweenLABEL=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,d2the input to this functionCOEFFICIENTS=1.0,-1.0the 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 actionsCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1,d3the input to this functionCOEFFICIENTS=-1.0,1.0the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=block1a 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=d2,d3the input to this functionCOEFFICIENTS=-1.0,1.0the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=block2a 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=d1,d2the arguments on which the bias is actingAT=2.5,2.5the positions of the wallKAPPA=100.0,100.0the force constant for the wallLABEL=constraina 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=block1,block2the arguments on which the bias is actingAT=0.0,0.0the positions of the wallKAPPA=1000.0,1000.0the force constant for the wallLABEL=conea 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=-2.5the lower bounds for the gridGRID_MAX=2.5the upper bounds for the gridGRID_BIN=1000the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density esimtationLABEL=hh ... 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=300the temperature at which you are operatingLABEL=ffa 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=hhthe grid you would like to print (can also use ARG for specifying what is being printed)FILE=histothe file on which to write the gridSTRIDE=10000000the 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=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=10000000the 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=10000the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARG=d1,d2,cvthe 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