Project ID: plumID:22.039
Source: urea_plumed.dat
Originally used with PLUMED version: 2.6.1
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=InterFace.cpp
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=PairEntropy.cpp
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=ManyAngle.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
W: 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=2401-11655:3
 
# Define the CV
MANY_ANGLEThis 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

MANY_ANGLEThis 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

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

INTERFACEThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=int
 CENTER=C
 Water=W
 R0CUT=0.8
 RWCUT=0.4
 R_0=0.5
 R_W=0.3
 C_0=5
... INTERFACE

Q6Calculate sixth order Steinhardt parameters. This action is a shortcut and it has hidden defaults. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=q6
 SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=C
 R_0The r_0 parameter of the switching function=0.60 
 MEAN calculate the mean of all the quantities
 LOWMEM this flag does nothing and is present only to ensure back-compatibility
... Q6

PAIRENTROPYCalculate the KL Entropy from the radial distribution function More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=s
 ATOMSthe atoms that are being used to calculate the RDF=C
 MAXRthe maximum distance to use for the rdf=0.6
 SIGMA an alternative method for specifying the bandwidth instead of using the BANDWIDTH keyword=0.05
... PAIRENTROPY

# Construct a bias potential using metadynamics

l1_1: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ma1.mean,ma2.mean,ma1.moment2,ma2.moment2,cn.morethan-1,cn.morethan-2,cn.moment-2,int,q6.mean,s COEFFICIENTS the coefficients of the arguments in your function=1.192779302597,-4.754418849945,0.035175766796,-0.366665005684,0.002653433941,0.011365669779,-0.020645860583,-0.000668735709,-0.072709567845,0.142931178212 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
l1_2: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ma1.mean,ma2.mean,ma1.moment2,ma2.moment2,cn.morethan-1,cn.morethan-2,cn.moment-2,int,q6.mean,s COEFFICIENTS the coefficients of the arguments in your function=-4.171144485474,-0.252191036940,0.253239363432,-0.522297024727,-0.006509369239,0.100738972425,-0.119564652443,0.000595316174,1.388457655907,-0.096874527633 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
l1r_1: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=l1_1 FUNCthe function you wish to evaluate=x+2.238606452942 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
l1r_2: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=l1_2 FUNCthe function you wish to evaluate=x+2.579712629318 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# load metaD

METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. 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=l1r_1,l1r_2 SIGMAthe widths of the Gaussian hills=0.2,0.2 HEIGHTthe heights of the Gaussian hills=10 BIASFACTORuse well tempered metadynamics and use this bias factor=150 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 PACEthe frequency for hill addition=2000
GRID_MINthe lower bounds for the grid=-5,-5 GRID_MAXthe upper bounds for the grid=5,20 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

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ma1.mean,ma2.mean,ma1.moment2,ma2.moment2,cn.morethan-1,cn.morethan-2,cn.moment-2,int,q6.mean,s,l1r_1,l1r_2,metad.bias,metad.rbias STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR