Project ID: plumID:23.034
Source: SS_model/plumed.dat
Originally used with PLUMED version: 2.7.2
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
# 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=ManyAnglePlus.cpp

# Define groups for the CV
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=centers.dat
C: 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=1-2400:8
O: 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=2-2400:8
N1: 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=3-2400:8
N2: 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=6-2400:8
 
# 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=C
 START=Ncenter
 END=O
 MAXR=0.6
 SIGMA=0.05,0.25
... PAIR_ORIENTATIONAL_ENTROPY

PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=s2
 CENTER=C
 START=N1
 END=N2
 MAXR=0.6
 SIGMA=0.05,0.125
 UP_DOWN_SYMMETRY
... PAIR_ORIENTATIONAL_ENTROPY

MANY_ANGLE_PLUSThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=ma1
 CENTER=C
 START=Ncenter
 END=O
 RCUT=1.0
 NOPBC
 MEAN
 MOMENT2
... MANY_ANGLE_PLUS

MANY_ANGLE_PLUSThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=ma2
 CENTER=C
 START=N1
 END=N2
 RCUT=1.0
 NOPBC
 MEAN
 MOMENT2
... MANY_ANGLE_PLUS

COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=cn SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=Ncenter
 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.6 D_MAX=0.8}
 MORE_THAN1calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=8.0 D_MAX=9.0}
 MORE_THAN2calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=11.0 D_MAX=12.0}
 MOMENTSthe list of moments that you would like to calculate=2
 LOWMEM this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER

# 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=5.0   # Height of the gaussians in energy units kJ/mol. This is around 2 kT. 1kT = 2.494339
 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=100.0   # 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=-15.0,-15.0   # The following three lines define a grid for the calculation of the bias potential. Use it **always**.
 GRID_MAXthe upper bounds for the grid=0.0,0.0
 GRID_BINthe number of bins for the grid=600,600
 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD

# 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