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

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
tested on master
# 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 definitions
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cv_definitions.dat

path: FUNCPATHGENERALThis function calculates path collective variables (PCVs) using an arbitrary combination of collective variables. More details ARGthe labels of the values from which the function is calculated=pp.proj,pp.ext,d1,d2,d3,d4 COEFFICIENTSCoefficients to be assigned to the CVs=9.3101e-02,2.4712e-01,2.5745e-02,1.2017e-01,7.4306e-02,1.2492e-01 REFERENCEColvar file needed to provide the CV milestones=COLVAR_PATH LAMBDALambda parameter required for smoothing=7.4143e+02

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

# Funnel
s_cent: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=3.0
beta_cent: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.5
wall_width: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.2
wall_buffer: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.15

lwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1
uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=4.5 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1

MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
        LABELa label for the action so that its output can be referenced in the input to other actions=wall_center
        ARGthe values input to this function=pp.proj,s_cent,beta_cent,wall_width,wall_buffer
        VARthe names to give each of the arguments in the function=s,sc,b,h,f
        FUNCthe function you wish to evaluate=h*(1./(1.+exp(b*(s-sc))))+f
        PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

scaling: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.0
spring: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1000.0

MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
        LABELa label for the action so that its output can be referenced in the input to other actions=wall_bias
        ARGthe values input to this function=pp.ext,spring,wall_center,scaling
        VARthe names to give each of the arguments in the function=z,k,zc,sf
        FUNCthe function you wish to evaluate=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sf)
        PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

finalbias: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=wall_bias

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

# Metadynamics
METADUsed to performed metadynamics on one or more collective variables. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=metad
 ARGthe labels of the scalars on which the bias will act=path.s,path.z
 SIGMAthe widths of the Gaussian hills=0.15,0.0004
 HEIGHTthe heights of the Gaussian hills=2.0
 PACEthe frequency for hill addition=1000
 FILE a file in which the list of added hills is stored=HILLS
 BIASFACTORuse well tempered metadynamics and use this bias factor=12.0
 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
 GRID_MINthe lower bounds for the grid=0.95,-0.02
 GRID_MAXthe upper bounds for the grid=16.05,0.20
 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.05,0.0002
 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f