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 onv2.10
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

# ==== GROUPS ====
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=1,2,3,4,5,6
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=9,12
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=15,16
H: 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=7,8,10,11,13,14

# ==== HEAVY ATOMS ====
C1: 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
C2: 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
C3: 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
C4: 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
C5: 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
C6: 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
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=9
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=12
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=15
O2: 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=16

c1c: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=C SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances 
c1n: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=N SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c1o: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=O SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c1h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c2c: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=C SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances 
c2n: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=N SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c2o: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=O SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c2h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c3c: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=C SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances 
c3n: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=N SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c3o: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=O SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c3h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c4c: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=C SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances 
c4n: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=N SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c4o: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=O SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c4h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c5c: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=C SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances 
c5n: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=N SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c5o: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=O SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c5h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c6c: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=C SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances 
c6n: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=N SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c6o: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=O SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
c6h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances

n1h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
n2h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances

o1h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=O1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances
o2h: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=O2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8} NOPBC ignore the periodic boundary conditions when calculating distances


# ==== PRINT STUFF ====
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=coordNumbers ARGthe labels of the values that you would like to print to the file=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