Project ID: plumID:20.016
Source: Naphthalene/plumed.dat
Originally used with PLUMED version: 2.6-dev
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
# Restart simulation. This command will append results of new simulations to the same output files, e.g. COLVAR.
# RESTART

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=PairOrientationalEntropy.cpp
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=PairOrientationalEntropyPerpendicular.cpp

# Define groups for the CV
C8: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=8-648:18 # Head
C9: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=9-648:18 # Head
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=centers.dat

# Define the CV

PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=s1
 CENTER=CENTERS
 START=STARTS
 END=ENDS
 MAXR=0.7
 SIGMA=0.05,0.125
 #REFERENCE_DENSITY=4.5
 UP_DOWN_SYMMETRY
 LOW_COMM
... PAIR_ORIENTATIONAL_ENTROPY

PAIR_ORIENTATIONAL_ENTROPY_PERPENDICULARThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=s2
 CENTER=CENTERS
 START1=STARTS
 END1=ENDS
 START2=C8
 END2=C9
 MAXR=0.7
 SIGMA=0.05,0.125
 #REFERENCE_DENSITY=4.5
 UP_DOWN_SYMMETRY
 LOW_COMM
... PAIR_ORIENTATIONAL_ENTROPY_PERPENDICULAR

# Construct a bias potential using 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=s1,s2   # Label of the CV
 PACEthe frequency for hill addition=500   # Pace in the deposition of the gaussians
 HEIGHTthe heights of the Gaussian hills=12.25   # Height of the gaussians in energy units kJ/mol. This is 2 kT.
 SIGMAthe widths of the Gaussian hills=0.2,0.2    # Width of the gaussian in CV units
 FILE a file in which the list of added hills is stored=HILLS   # File where the information of the gaussians is printed
 BIASFACTORuse well tempered metadynamics and use this bias factor=200.0   # Bias factor in well tempered simulations
 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0   # Temperature in Kelvin. Only needed for well tempered simulations
 GRID_MINthe lower bounds for the grid=-20.0,-20.0   # The following three lines define a grid for the calculation of the bias potential. Use it **always**.
 GRID_MAXthe upper bounds for the grid=0.,0.
 GRID_BINthe number of bins for the grid=1000,1000
 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD

# Restraint the volume
vol: VOLUMECalculate the volume the simulation box. More details

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=vol ATthe positions of the wall=12.0 KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=1 LABELa label for the action so that its output can be referenced in the input to other actions=uwall

# Print value of the CV and bias to a file named COLVAR
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR