Project ID: plumID:22.032
Source: plumed.dat
Originally used with PLUMED version: 2.7
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
PATHMSDThis Colvar calculates path collective variables. More detailsREFERENCE=path.pdbthe pdb is needed to provide the various milestonesLAMBDA=1498the lambda parameter is needed for smoothing, is in the units of plumedNEIGH_STRIDE=4how often the neighbor list needs to be calculated in time unitsNEIGH_SIZE=8size of the neighbor listLABEL=patha label for the action so that its output can be referenced in the input to other actionsCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=path.zzzthe input to this functionFUNC=sqrt(xthe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=path_za label for the action so that its output can be referenced in the input to other actionsDRRUsed to performed extended-system adaptive biasing force(eABF) More detailsARG=path.sssthe input for this action is the scalar output from one or more other actionsFULLSAMPLES=2000number of samples in a bin prior to application of the ABFGRID_MIN=1the lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)GRID_MAX=49the upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)GRID_SPACING=0.1the approximate grid spacing (to be used as an alternative or together with GRID_BIN)TEMP=310the system temperature - needed when FRICTION is presentFRICTION=8.0add a friction to the variable, similar to extended Langevin Damping in ColvarsTAU=0.5specifies relaxation time on each of variables are, similar to extended Time Constant in ColvarsTEXTOUTPUTuse text output for grad and count files instead of boost::serialization binary outputOUTPUTFREQ=200000write results to a file every N stepsHISTORYFREQ=2000000save history to a file every N stepsLABEL=drra label for the action so that its output can be referenced in the input to other actionsMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=drr.path.sss_fictthe input for this action is the scalar output from one or more other actionsSIGMA=0.5the widths of the Gaussian hillsHEIGHT=1.8the heights of the Gaussian hillsPACE=500the frequency for hill additionGRID_MIN=0the lower bounds for the gridGRID_MAX=50the upper bounds for the gridGRID_SPACING=0.1the approximate grid spacing (to be used as an alternative or together with GRID_BIN)BIASFACTOR=20use well tempered metadynamics and use this bias factorTEMP=310the system temperature - this is only needed if you are doing well-tempered metadynamicsFILE=HILLSa file in which the list of added hills is storedLABEL=metada label for the action so that its output can be referenced in the input to other actionsCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=path_zthe input to this functionFUNC=(0.27-x)^-1the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=uwz_arga label for the action so that its output can be referenced in the input to other actionsBIASVALUETakes the value of one variable and use it as a bias More detailsARG=uwz_argthe input for this action is the scalar output from one or more other actionsLABEL=uw_path_za label for the action so that its output can be referenced in the input to other actionsCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=path.sssthe input to this functionFUNC=(49-x)^-1the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=uws_arga label for the action so that its output can be referenced in the input to other actionsBIASVALUETakes the value of one variable and use it as a bias More detailsARG=uws_argthe input for this action is the scalar output from one or more other actionsLABEL=uw_sssa label for the action so that its output can be referenced in the input to other actionsCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=path.sssthe input to this functionFUNC=(x-1)^-1the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=lws_arga label for the action so that its output can be referenced in the input to other actionsBIASVALUETakes the value of one variable and use it as a bias More detailsARG=lws_argthe input for this action is the scalar output from one or more other actionsLABEL=lw_sssa label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=plumed.logthe name of the file on which to output these quantitiesFMT=%12.4fthe format that should be used to output real numbersFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1000the frequency with which all the open files should be flushed