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
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#! 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
#UNITSUNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths
# ==== 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 detailsATOMS=1,2,3,4,5,6 N:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=9,12 O:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=15,16 H:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=7,8,10,11,13,14the numerical indexes for the set of atoms in the group
# ==== 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 detailsATOMS=1 C2:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=2 C3:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=3 C4:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=4 C5:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=5 C6:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=6 N1:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=9 N2:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=12 O1:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=15 O2:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=16the numerical indexes for the set of atoms in the group
c1c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=C1First list of atomsGROUPB=CSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc1n:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C1First list of atomsGROUPB=NSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc1o:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C1First list of atomsGROUPB=OSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc1h:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C1First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc2c:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C2First list of atomsGROUPB=CSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc2n:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C2First list of atomsGROUPB=NSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc2o:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C2First list of atomsGROUPB=OSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc2h:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C2First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc3c:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C3First list of atomsGROUPB=CSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc3n:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C3First list of atomsGROUPB=NSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc3o:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C3First list of atomsGROUPB=OSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc3h:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C3First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc4c:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C4First list of atomsGROUPB=CSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc4n:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C4First list of atomsGROUPB=NSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc4o:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C4First list of atomsGROUPB=OSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc4h:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C4First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc5c:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C5First list of atomsGROUPB=CSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc5n:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C5First list of atomsGROUPB=NSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc5o:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C5First list of atomsGROUPB=OSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc5h:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C5First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc6c:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C6First list of atomsGROUPB=CSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc6n:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C6First list of atomsGROUPB=NSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc6o:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C6First list of atomsGROUPB=OSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCc6h:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=C6First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCignore the periodic boundary conditions when calculating distances
n1h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=N1First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCn2h:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=N2First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCignore the periodic boundary conditions when calculating distances
o1h:COORDINATIONCalculate coordination numbers. More detailsGROUPA=O1First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCo2h:ignore the periodic boundary conditions when calculating distancesCOORDINATIONCalculate coordination numbers. More detailsGROUPA=O2First list of atomsGROUPB=HSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=1.2 NN=6 MM=8}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNOPBCignore the periodic boundary conditions when calculating distances
# ==== PRINT STUFF ====Print quantities to a file. More detailsFILE=coordNumbersthe name of the file on which to output these quantitiesARG=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,c6hthe input for this action is the scalar output from one or more other actionsSTRIDE=50the frequency with which the quantities of interest should be output