Project ID: plumID:19.080
Source: clch3cl/ch-sample/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 energyCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.10The r_0 parameter of the switching functionNN=12The n parameter of the switching functionLABEL=dis1a label for the action so that its output can be referenced in the input to other actionsCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.10The r_0 parameter of the switching functionNN=12The n parameter of the switching functionLABEL=dis2a label for the action so that its output can be referenced in the input to other actionsCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.10The r_0 parameter of the switching functionNN=12The n parameter of the switching functionLABEL=dis3a 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=dis1,dis2,dis3the input to this functionCOEFFICIENTS=0.333,0.333,0.333the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=nma 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=nmthe quantity that is being averagedGRID_MIN=0.0the lower bounds for the gridGRID_MAX=1.0the upper bounds for the gridGRID_BIN=500the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density esimtationLABEL=targetdist ... 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=targetdistthe 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=targetdistthe 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=20000the 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=20000the 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=200the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARG=dis1,nmthe input for this action is the scalar output from one or more other actionsSTRIDE=200the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities