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 onv2.9
tested onmaster
tested on master
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=InterFace.cpp

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=PairOrientationalEntropy.cpp

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=ManyAngle.cpp

# Define groups for the CV
#INCLUDE FILE=centers.dat
N: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-720:10
CA: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=2-720:10
C: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=3-720:10
O1: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=5-720:10
O: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=4-720:10
HA1: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=8-720:10
W: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=721-4321:3

PAIR_ORIENTATIONAL_ENTROPY
This 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_ENTROPY
This 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_ANGLE
This 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_ANGLE
This 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

COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cn 
SPECIES
this keyword is used for colvars such as coordination number
=CA
 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.6 D_MAX=0.8}
 
MORE_THAN1
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=8.0 D_MAX=9.0}
 
MORE_THAN2
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=11.0 D_MAX=12.0}
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility

... COORDINATIONNUMBER

INTERFACE
This 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

Q4
Calculate fourth order Steinhardt parameters. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=q4
 
SPECIES
this keyword is used for colvars such as coordination number
=CA
 
R_0
The 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

Q6
Calculate sixth order Steinhardt parameters. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=q6
 
SPECIES
this keyword is used for colvars such as coordination number
=CA
 
R_0
The 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: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the 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 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
l1_2: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the 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 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
l1r_1: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=l1_1 
FUNC
the function you wish to evaluate
=x+0.375591367483 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
l1r_2: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=l1_2 
FUNC
the function you wish to evaluate
=x+0.160054937005 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...

LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad

ARG
the input for this action is the scalar output from one or more other actions
=l1r_1,l1r_2 
SIGMA
the widths of the Gaussian hills
=1.15,1.15 
HEIGHT
the heights of the Gaussian hills
=5.0 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=100 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0 
PACE
the frequency for hill addition
=1000

GRID_MIN
the lower bounds for the grid
=-10,-10 
GRID_MAX
the 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

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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 
FILE
the name of the file on which to output these quantities
=COLVAR