Project ID: plumID:22.039
Source: glycine_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
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=PairOrientationalEntropy.cpp
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=ManyAngle.cpp

# Define groups for the CV
#INCLUDE FILE=centers.dat
N: 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=1-720:10
CA: 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=2-720:10
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=3-720:10
O1: 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=5-720:10
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=4-720:10
HA1: 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=8-720:10
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=721-4321:3

PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=s1
 #Should really be the geometric center, but will try just using the Ca position first
 CENTER=CA
 START=C
 END=N
 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=CA
 START=CA
 END=HA1
 MAXR=0.6
 SIGMA=0.05,0.125
 #UP_DOWN_SYMMETRY
... PAIR_ORIENTATIONAL_ENTROPY

# Define the CV
MANY_ANGLEThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=ma1
 CENTER=CA
 START=C
 END=N
 RCUT=0.64
 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_6
 CENTER=CA
 START=CA
 END=HA1
 RCUT=0.64
 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=CA
 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}
 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=CA
 Water=W
 R0CUT=0.8
 RWCUT=0.4
 R_0=0.5
 R_W=0.3
 C_0=5
... INTERFACE

Q4Calculate fourth 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=q4
 SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=CA
 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
... Q4

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=CA
 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

l1_1: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=s1,s2,ma1.mean,ma1.moment2,ma2_6.mean,ma2_6.moment2,cn.morethan-1,cn.morethan-2,int,q4.mean,q6.mean COEFFICIENTS the coefficients of the arguments in your function=0.268421709538,-0.165572479367,1.218452692032,-0.409345626831,-2.642394781113,1.740240216255,0.001185834059,0.033699873835,-0.008368298411,-0.443194448948,0.387469917536 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=s1,s2,ma1.mean,ma1.moment2,ma2_6.mean,ma2_6.moment2,cn.morethan-1,cn.morethan-2,int,q4.mean,q6.mean COEFFICIENTS the coefficients of the arguments in your function=-0.562040388584,-0.074013128877,-3.022350788116,1.183155536652,-0.754271864891,2.320541858673,-0.045729581267,-0.026172904298,-0.023710954934,0.582593202591,1.333106040955 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+0.375591367483 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+0.160054937005 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

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=1.15,1.15 HEIGHTthe heights of the Gaussian hills=5.0 BIASFACTORuse well tempered metadynamics and use this bias factor=100 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 PACEthe frequency for hill addition=1000
GRID_MINthe lower bounds for the grid=-10,-10 GRID_MAXthe upper bounds for the grid=10,10
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=s1,s2,ma1.mean,ma1.moment2,ma2_6.mean,ma2_6.moment2,cn.morethan-1,cn.morethan-2,int,q4.mean,q6.mean,l1r_1,l1r_2,metad.bias,metad.rbias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR