Project ID: plumID:23.033
Source: plumed_inputs/parallel_hairpin_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/GGGTTAGGG/parallel_propeller_aaa-aaa.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=1-293the 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 (gHBfix_typesTable.dat) and eta/scaling parameters are specified (gHBfix_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=19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,22,22,23,23,19,19,22,22,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,55,55,56,56,52,52,55,55,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,88,88,89,89,85,85,88,88,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,181,181,181,182,182,182,181,181,181,182,182,182,181,181,181,182,182,182,181,181,182,182,181,181,182,182,181,181,181,182,182,182,181,181,181,182,182,182,181,181,181,182,182,182,214,214,214,217,217,217,218,218,218,214,214,214,217,217,217,218,218,218,214,214,214,217,217,217,218,218,218,214,214,217,217,218,218,214,214,217,217,218,218,214,214,214,217,217,217,218,218,218,214,214,214,217,217,217,218,218,218,214,214,214,217,217,217,218,218,218,247,247,247,250,250,250,251,251,251,247,247,247,250,250,250,251,251,251,247,247,247,250,250,250,251,251,251,247,247,250,250,251,251,247,247,250,250,251,251,247,247,247,250,250,250,251,251,251,247,247,247,250,250,250,251,251,251,247,247,247,250,250,250,251,251,251,280,280,280,283,283,283,284,284,284,280,280,280,283,283,283,284,284,284,280,280,280,283,283,283,284,284,284,280,280,283,283,284,284,280,280,283,283,284,284,280,280,280,283,283,283,284,284,284,280,280,280,283,283,283,284,284,284,280,280,280,283,283,283,284,284,284First list of atomsGROUPB=50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,245,242,252,245,242,252,245,242,252,278,275,285,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,245,242,252,245,242,252,245,242,252,278,275,285,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,245,242,252,245,242,252,245,242,252,278,275,285,278,275,285,278,275,285,17,14,24,50,47,57,83,80,90,151,155,177,183,186,212,209,219,245,242,252,278,275,285,17,14,24,50,47,57,83,80,90,119,123,177,183,186,212,209,219,245,242,252,278,275,285,17,14,24,17,14,24,50,47,57,50,47,57,83,80,90,83,80,90,119,123,119,123,151,155,151,155,212,209,219,212,209,219,245,242,252,245,242,252,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,245,242,252,245,242,252,245,242,252,278,275,285,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,278,275,285,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,245,242,252,245,242,252,245,242,252Second 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_hairpin.datthe value of TYPES in the switching functionPARAMS=./gHBfix_scalingParameters_hairpin.datthe value of PARAMS in the switching function
# scaling of gHBfix in replicas. reference replica has 2kcal/mol gHBfix. coefs=lambdas (scalingTable has 1.00) 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:{2.0000000,1.9092000,1.8225220,1.7397800,1.6607940,1.5853940,1.5134160,1.4447080,1.3791180,1.3165060,1.2567360,1.1996800}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-7,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.@lcs-8,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.REFERENCE=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdba file in pdb format containing the reference structure and the atoms involved in the CVCUTOFF=3.2 DISTg5end: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/GGGTTAGGG/parallel_propeller_aaa-aaa.pdba file in pdb format containing the reference structure and the atoms involved in the CVCUTOFF=3.2 DISTg3end: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-7,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.@lcs-8,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.REFERENCE=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.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,DISTg5end,DISTg3endthe input to this functionCOEFFICIENTS=6,-3,-3the coefficients of the arguments in your functionPOWERS=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=0.40824829 #COEF=sqrt(1/6)the 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-7,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information.@lcs-8,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.REFERENCE=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.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=4.0the 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=tot_1,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 quantitiesPrint 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 output