Project ID: plumID:23.033
Source: plumed_inputs/G4_full_gHBfix_plumed.dat
Originally used with PLUMED version: 2.5.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
# uncomment the following LOAD line if using older version of PLUMED: # LOAD FILE=./GHBFIX.cppMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=../reference_structures/G4/G4_full.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-491the atoms that make up a molecule that you wish to align
# gHBfix SECTION #! GroupA and GroupB are all relevant donors and acceptors. D_0, D_MAX and C have to be defined according to the gHBfix switching function - default values printed (Kuehrova, Mlynsky et al., JCTC 2019). Each relevant type of donor and acceptor are labeled with an integer (typesTable.dat) and eta/scaling parameters are specified (scalingParameters.dat). group_1:GHBFIXCalculate the GHBFIX interaction energy among GROUPA and GROUPB More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,117,117,117,118,118,118,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,150,150,150,153,153,153,154,154,154,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,183,183,183,186,186,186,187,187,187,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,216,216,216,219,219,219,220,220,220,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,248,248,248,249,249,249,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,281,281,281,284,284,284,285,285,285,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,314,314,314,317,317,317,318,318,318,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,347,347,347,350,350,350,351,351,351,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,379,379,379,380,380,380,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,412,412,412,415,415,415,416,416,416,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,445,445,445,448,448,448,449,449,449,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482,478,478,478,481,481,481,482,482,482First list of atomsGROUPB=50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,50,47,57,50,47,57,83,80,90,83,80,90,148,145,155,148,145,155,181,178,188,181,178,188,214,211,221,214,211,221,244,250,253,244,250,253,279,276,286,279,276,286,312,309,319,312,309,319,345,342,352,345,342,352,375,381,384,375,381,384,410,407,417,410,407,417,443,440,450,443,440,450,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,50,47,57,50,47,57,83,80,90,83,80,90,113,119,122,113,119,122,148,145,155,148,145,155,181,178,188,181,178,188,214,211,221,214,211,221,279,276,286,279,276,286,312,309,319,312,309,319,345,342,352,345,342,352,375,381,384,375,381,384,410,407,417,410,407,417,443,440,450,443,440,450,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,50,47,57,50,47,57,83,80,90,83,80,90,113,119,122,113,119,122,148,145,155,148,145,155,181,178,188,181,178,188,214,211,221,214,211,221,244,250,253,244,250,253,279,276,286,279,276,286,312,309,319,312,309,319,345,342,352,345,342,352,410,407,417,410,407,417,443,440,450,443,440,450,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,443,440,450,443,440,450,443,440,450,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,476,473,483,476,473,483,476,473,483,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,113,119,122,113,119,122,113,119,122,148,145,155,148,145,155,148,145,155,181,178,188,181,178,188,181,178,188,214,211,221,214,211,221,214,211,221,244,250,253,244,250,253,244,250,253,279,276,286,279,276,286,279,276,286,312,309,319,312,309,319,312,309,319,345,342,352,345,342,352,345,342,352,375,381,384,375,381,384,375,381,384,410,407,417,410,407,417,410,407,417,443,440,450,443,440,450,443,440,450Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)D_0=0.2the value of D_0 in the switching functionD_MAX=0.3the value of D_MAX in the switching functionC=0.8the value of C in the switching functionTYPES=gHBfix_typesTable_g4.datthe value of TYPES in the switching functionPARAMS=gHBfix_scalingParameters_g4.datthe value of PARAMS in the switching function
# scaling of gHBfix in replicas. reference replica has 2kcal/mol gHBfix. coefs=lambdas (scalingTable has 2.00) tot_1:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=group_1the input to this functionCOEFFICIENTS=the coefficients of the arguments in your function@replicas:{1.045400,1.022700,1.000000,0.976270,0.954600,0.931947,0.911261,0.869890,0.830397,0.792697,0.756708,0.722354,0.689559,0.658253,0.628368,0.599840}This keyword specifies that different replicas have different values for this quantity. See here for more details.PERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionBIASVALUETakes the value of one variable and use it as a bias More detailsARG=tot_1the input for this action is the scalar output from one or more other actionsLABEL=all_group_1a label for the action so that its output can be referenced in the input to other actions
# biasing eRMSD with augmented cutoff: DISTfull:ERMSDCalculate eRMSD with respect to a reference structure. More detailsATOMS=the list of atoms (use lcs)@lcs-1,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information.@lcs-2,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information.@lcs-3,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information.@lcs-5,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information.@lcs-6,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information.@lcs-7,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.@lcs-9,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.@lcs-10,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information.@lcs-11,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information.@lcs-13,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information.@lcs-14,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information.@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.REFERENCE=../reference_structures/G4/G4_full.pdba file in pdb format containing the reference structure and the atoms involved in the CVCUTOFF=3.2 DISTpart1:only pairs of atoms closer than CUTOFF are considered in the calculationERMSDCalculate eRMSD with respect to a reference structure. More detailsATOMS=the list of atoms (use lcs)@lcs-1,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information.@lcs-2,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information.@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information.REFERENCE=../reference_structures/G4/G4_full.pdba file in pdb format containing the reference structure and the atoms involved in the CVCUTOFF=3.2 DISTpart2:only pairs of atoms closer than CUTOFF are considered in the calculationERMSDCalculate eRMSD with respect to a reference structure. More detailsATOMS=the list of atoms (use lcs)@lcs-5,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information.@lcs-6,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information.@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.REFERENCE=../reference_structures/G4/G4_full.pdba file in pdb format containing the reference structure and the atoms involved in the CVCUTOFF=3.2 DISTpart3:only pairs of atoms closer than CUTOFF are considered in the calculationERMSDCalculate eRMSD with respect to a reference structure. More detailsATOMS=the list of atoms (use lcs)@lcs-9,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.@lcs-10,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information.@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information.REFERENCE=../reference_structures/G4/G4_full.pdba file in pdb format containing the reference structure and the atoms involved in the CVCUTOFF=3.2 DISTpart4:only pairs of atoms closer than CUTOFF are considered in the calculationERMSDCalculate eRMSD with respect to a reference structure. More detailsATOMS=the list of atoms (use lcs)@lcs-13,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information.@lcs-14,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information.@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.REFERENCE=../reference_structures/G4/G4_full.pdba file in pdb format containing the reference structure and the atoms involved in the CVCUTOFF=3.2only pairs of atoms closer than CUTOFF are considered in the calculationCOMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=DDa label for the action so that its output can be referenced in the input to other actionsARG=DISTfull,DISTpart1,DISTpart2,DISTpart3,DISTpart4the input to this functionCOEFFICIENTS=12,-3,-3,-3,-3the coefficients of the arguments in your functionPOWERS=2,2,2,2,2the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=interDa label for the action so that its output can be referenced in the input to other actionsARG=DDthe input to this functionPOWERS=0.5the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionCOEFFICIENTS=0.288675135 #COEF=sqrt(1/12the coefficients of the arguments in your function
# eRMSD with standard cutoff (2.4), used for monitoring only: DIST1:ERMSDCalculate eRMSD with respect to a reference structure. More detailsATOMS=the list of atoms (use lcs)@lcs-1,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information.@lcs-2,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information.@lcs-3,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information.@lcs-5,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information.@lcs-6,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information.@lcs-7,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.@lcs-9,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.@lcs-10,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information.@lcs-11,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information.@lcs-13,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information.@lcs-14,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information.@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.REFERENCE=../reference_structures/G4/G4_full.pdba file in pdb format containing the reference structure and the atoms involved in the CV
# metadynamics metad:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=interDthe input for this action is the scalar output from one or more other actionsPACE=250the frequency for hill additionTAU=70in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauSIGMA=0.1the widths of the Gaussian hillsFILE=HILLSa file in which the list of added hills is storedTEMP=298the system temperature - this is only needed if you are doing well-tempered metadynamicsBIASFACTOR=15use well tempered metadynamics and use this bias factorGRID_MIN=0the lower bounds for the gridGRID_MAX=5.0the upper bounds for the gridGRID_SPACING=0.02the approximate grid spacing (to be used as an alternative or together with GRID_BIN)Print quantities to a file. More detailsARG=interD,DIST1,metad.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=250the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=all_group_1.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=250the frequency with which the quantities of interest should be outputFILE=check_ghbfix.datthe name of the file on which to output these quantities