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
#! 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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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={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