Project ID: plumID:21.028
Source: benzoquinone_PT/1_unbiased/plumed.dat
Originally used with PLUMED version: 2.7
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
#! vim:ft=plumed

# input file for unbiased intramolecular double proton transfer in 2,5-diamino-1,4-benzoquinone
# we can use the coordination numbers of the heavy atoms! # We take them of the type CC, CH, CO, CO, NH, OH
#UNITS
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
# ==== GROUPS ==== 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
=1,2,3,4,5,6 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
=9,12 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
=15,16 H:
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
=7,8,10,11,13,14
# ==== HEAVY ATOMS ==== C1:
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 C2:
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 C3:
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 C4:
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 C5:
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 C6:
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
=6 N1:
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
=9 N2:
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
=12 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
=15 O2:
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
=16
c1c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C1
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=C
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c1n:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C1
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=N
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c1o:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C1
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=O
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c1h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C1
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c2c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C2
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=C
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c2n:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C2
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=N
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c2o:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C2
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=O
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c2h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C2
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c3c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C3
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=C
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c3n:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C3
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=N
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c3o:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C3
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=O
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c3h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C3
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c4c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C4
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=C
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c4n:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C4
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=N
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c4o:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C4
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=O
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c4h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C4
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c5c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C5
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=C
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c5n:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C5
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=N
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c5o:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C5
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=O
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c5h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C5
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c6c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C6
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=C
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c6n:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C6
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=N
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c6o:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C6
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=O
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
c6h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=C6
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances

n1h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=N1
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
n2h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=N2
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances

o1h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=O1
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances
o2h:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=O2
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=H
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}
NOPBC
ignore the periodic boundary conditions when calculating distances

# ==== PRINT STUFF ====
PRINT
Print quantities to a file. More details
FILE
the name of the file on which to output these quantities
=coordNumbers
ARG
the input for this action is the scalar output from one or more other actions
=n1h,n2h,o1h,o2h,c1c,c1n,c1o,c1h,c2c,c2n,c2o,c2h,c3c,c3n,c3o,c3h,c4c,c4n,c4o,c4h,c5c,c5n,c5o,c5h,c6c,c6n,c6o,c6h
STRIDE
the frequency with which the quantities of interest should be output
=50