**Project ID:** plumID:20.012

**Source:** COMet_Path/plumed.dat

**Originally used with PLUMED version:** 2.4.2

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

# Plumed file generated by the COMet script

#LOAD FILE=FuncPathGeneral.cpp # Now part of Plumed, not necessary to load it

# The file containing the CV definitionsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=cv_definitions.datfile to be includedpath:FUNCPATHGENERALThis function calculates path collective variables (PCVs) using an arbitrary combination of collective variables. More detailsARG=the input for this action is the scalar output from one or more other actionspp.proj,pp.ext,d1,d2,d3,d4COEFFICIENTS=9.3101e-02,2.4712e-01,2.5745e-02,1.2017e-01,7.4306e-02,1.2492e-01Coefficients to be assigned to the CVsREFERENCE=COLVAR_PATHColvar file needed to provide the CV milestonesLAMBDA=7.4143e+02Lambda parameter required for smoothing

# The file containing the CV restraints #INCLUDE FILE=restraints.dat

# Funnels_cent:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=3.0The values of the constantsbeta_cent:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=1.5The values of the constantswall_width:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=1.2The values of the constantswall_buffer:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=0.15The values of the constantslwall:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionspp.projAT=0.0the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a walluwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionspp.projAT=4.5the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallMATHEVAL...An alias to the ef CUSTOM function. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionswall_centerARG=the input for this action is the scalar output from one or more other actionspp.proj,s_cent,beta_cent,wall_width,wall_bufferVAR=s,sc,b,h,fthe names to give each of the arguments in the functionFUNC=h*(1./(1.+exp(b*(s-sc))))+fthe function you wish to evaluatePERIODIC=NO ... MATHEVALif the output of your function is periodic then you should specify the periodicity of the functionscaling:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=1.0The values of the constantsspring:CONSTANTReturn one or more constant quantities with or without derivatives. More detailsVALUES=1000.0The values of the constantsMATHEVAL...An alias to the ef CUSTOM function. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionswall_biasARG=the input for this action is the scalar output from one or more other actionspp.ext,spring,wall_center,scalingVAR=z,k,zc,sfthe names to give each of the arguments in the functionFUNC=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sfthe function you wish to evaluatePERIODIC=NO ... MATHEVALif the output of your function is periodic then you should specify the periodicity of the functionfinalbias:BIASVALUETakes the value of one variable and use it as a bias More detailsARG=the input for this action is the scalar output from one or more other actionswall_bias

#zwall: UPPER_WALLS ARG=path.z AT=0.1 KAPPA=1000000

# MetadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsmetadARG=the input for this action is the scalar output from one or more other actionspath.s,path.zSIGMA=0.15,0.0004the widths of the Gaussian hillsHEIGHT=2.0the heights of the Gaussian hillsPACE=1000the frequency for hill additionFILE=HILLSa file in which the list of added hills is storedBIASFACTOR=12.0use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=0.95,-0.02the lower bounds for the gridGRID_MAX=16.05,0.20the upper bounds for the gridGRID_SPACING=0.05,0.0002the approximate grid spacing (to be used as an alternative or together with GRID_BIN)CALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]Print 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=COLVARthe name of the file on which to output these quantitiesFMT=%8.4fthe format that should be used to output real numbers