Project ID: plumID:21.051
Source: plumed-nest/ST-MetaD/GAGA_gHBfix_0.5-0.5/plumed.4.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# vim:ft=plumed# choose units - by default PLUMED uses kj/mol, nm, and ps # UNITS ENERGY=kcal/mol LENGTH=AEnables syntax highlighting for PLUMED files in vim. See here for more details.
# UNTS !!!!!!!!!
# PDB that provides information on the molecules that are present in your system.MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=GAGA_native.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=1-263the atoms that make up a molecule that you wish to align
#################################################################################################### # gHBfix RESTRAINT SECTION ####################################################################################################
group_nh_n:COORDINATIONCalculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=19,22,23,19,19,22,22,23,23,19,19,19,22,22,22,23,23,23,19,19,22,22,23,23,19,19,19,22,22,22,23,23,23,19,19,22,22,23,23,19,22,23,52,52,53,53,52,52,53,53,52,52,52,53,53,53,52,52,53,53,52,52,52,53,53,53,52,52,53,53,52,53,84,84,87,87,88,88,84,87,88,84,84,84,87,87,87,88,88,88,84,84,87,87,88,88,84,84,84,87,87,87,88,88,88,84,84,87,87,88,88,84,87,88,117,117,118,118,117,118,117,117,118,118,117,117,118,118,117,117,117,118,118,118,117,117,118,118,117,118,151,151,154,154,155,155,151,154,155,151,151,154,154,155,155,151,151,151,154,154,154,155,155,155,151,151,151,154,154,154,155,155,155,151,151,154,154,155,155,151,154,155,184,184,185,185,184,185,184,184,185,185,184,184,184,185,185,185,184,184,185,185,184,184,185,185,184,185,218,218,221,221,222,222,218,221,222,218,218,221,221,222,222,218,218,218,221,221,221,222,222,222,218,218,221,221,222,222,218,218,218,221,221,221,222,222,222,218,221,222,251,251,252,252,251,252,251,251,252,252,251,251,251,252,252,252,251,251,252,252,251,251,251,252,252,252,251,251,252,252First list of atomsGROUPB=54,54,54,79,89,79,89,79,89,113,119,122,113,119,122,113,119,122,146,156,146,156,146,156,180,186,189,180,186,189,180,186,189,213,223,213,223,213,223,253,253,253,14,24,14,24,79,89,79,89,113,119,122,113,119,122,146,156,146,156,180,186,189,180,186,189,213,223,213,223,253,253,14,24,14,24,14,24,54,54,54,113,119,122,113,119,122,113,119,122,146,156,146,156,146,156,180,186,189,180,186,189,180,186,189,213,223,213,223,213,223,253,253,253,14,24,14,24,54,54,79,89,79,89,146,156,146,156,180,186,189,180,186,189,213,223,213,223,253,253,14,24,14,24,14,24,54,54,54,79,89,79,89,79,89,113,119,122,113,119,122,113,119,122,180,186,189,180,186,189,180,186,189,213,223,213,223,213,223,253,253,253,14,24,14,24,54,54,79,89,79,89,113,119,122,113,119,122,146,156,146,156,213,223,213,223,253,253,14,24,14,24,14,24,54,54,54,79,89,79,89,79,89,113,119,122,113,119,122,113,119,122,146,156,146,156,146,156,180,186,189,180,186,189,180,186,189,253,253,253,14,24,14,24,54,54,79,89,79,89,113,119,122,113,119,122,146,156,146,156,180,186,189,180,186,189,213,223,213,223Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={MATHEVAL FUNC=((-2092.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.3-x)+((-2092.0000000000)*(0.1)*(2*x-0.5))*step(x-0.3)+((2615.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.28-x)+((2615.0000000000)*(0.08)*(2*x-0.48))*step(x-0.28) R_0=1.0}This keyword is used if you want to employ an alternative to the continuous switching function defined above
group_nh_o:COORDINATIONCalculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=19,22,23,19,22,23,19,22,23,19,22,23,19,22,23,52,53,52,53,52,53,52,53,52,53,84,87,88,84,87,88,84,87,88,84,87,88,84,87,88,117,118,117,118,117,118,117,118,117,118,117,118,151,154,155,151,154,155,151,154,155,151,154,155,151,154,155,184,185,184,185,184,185,184,185,184,185,184,185,218,221,222,218,221,222,218,221,222,218,221,222,218,221,222,251,252,251,252,251,252,251,252,251,252First list of atomsGROUPB=56,56,56,82,82,82,149,149,149,216,216,216,255,255,255,17,17,82,82,149,149,216,216,255,255,17,17,17,56,56,56,149,149,149,216,216,216,255,255,255,17,17,56,56,82,82,149,149,216,216,255,255,17,17,17,56,56,56,82,82,82,216,216,216,255,255,255,17,17,56,56,82,82,149,149,216,216,255,255,17,17,17,56,56,56,82,82,82,149,149,149,255,255,255,17,17,56,56,82,82,149,149,216,216Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={MATHEVAL FUNC=((-2092.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.3-x)+((-2092.0000000000)*(0.1)*(2*x-0.5))*step(x-0.3)+((2615.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.28-x)+((2615.0000000000)*(0.08)*(2*x-0.48))*step(x-0.28) R_0=1.0}This keyword is used if you want to employ an alternative to the continuous switching function defined above
group_oh_nbo:COORDINATIONCalculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,62,62,62,62,62,62,62,62,62,62,62,62,62,62,96,96,96,96,96,96,96,96,96,96,96,96,96,96,129,129,129,129,129,129,129,129,129,129,129,129,129,129,163,163,163,163,163,163,163,163,163,163,163,163,163,163,196,196,196,196,196,196,196,196,196,196,196,196,196,196,230,230,230,230,230,230,230,230,230,230,230,230,230,230,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263First list of atomsGROUPB=34,35,34,35,65,66,65,66,99,100,99,100,132,133,132,133,166,167,166,167,199,200,199,200,233,234,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,34,35,65,66,65,66,99,100,99,100,132,133,132,133,166,167,166,167,199,200,199,200,233,234,233,234Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={MATHEVAL FUNC=((-2092.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.3-x)+((-2092.0000000000)*(0.1)*(2*x-0.5))*step(x-0.3)+((2615.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.28-x)+((2615.0000000000)*(0.08)*(2*x-0.48))*step(x-0.28) R_0=1.0}This keyword is used if you want to employ an alternative to the continuous switching function defined above
group_oh_bo:COORDINATIONCalculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcGROUPA=1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,1,62,62,62,62,62,62,62,62,62,62,62,62,62,96,96,96,96,96,96,96,96,96,96,96,96,96,129,129,129,129,129,129,129,129,129,129,129,129,129,163,163,163,163,163,163,163,163,163,163,163,163,163,196,196,196,196,196,196,196,196,196,196,196,196,196,230,230,230,230,230,230,230,230,230,230,230,230,230,261,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,263First list of atomsGROUPB=32,36,63,36,63,67,97,67,97,101,130,101,130,134,164,134,164,168,197,168,197,201,231,201,231,235,235,32,36,67,97,101,130,134,164,168,197,201,231,235,32,36,63,67,101,130,134,164,168,197,201,231,235,32,36,63,67,97,101,134,164,168,197,201,231,235,32,36,63,67,97,101,130,134,168,197,201,231,235,32,36,63,67,97,101,130,134,164,168,201,231,235,32,36,63,67,97,101,130,134,164,168,197,201,235,32,32,36,63,36,63,67,97,67,97,101,130,101,130,134,164,134,164,168,197,168,197,201,231,201,231,235,235Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={MATHEVAL FUNC=((-2092.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.3-x)+((-2092.0000000000)*(0.1)*(2*x-0.5))*step(x-0.3)+((2615.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.28-x)+((2615.0000000000)*(0.08)*(2*x-0.48))*step(x-0.28) R_0=1.0}This keyword is used if you want to employ an alternative to the continuous switching function defined above
tot_NH-N:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=group_nh_nthe input to this functionCOEFFICIENTS=0.415199the coefficients of the arguments in your functionPERIODIC=NO tot_NH-O:if 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 detailsARG=group_nh_othe input to this functionCOEFFICIENTS=0.415199the coefficients of the arguments in your functionPERIODIC=NO tot_OH-nbO:if 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 detailsARG=group_oh_nbothe input to this functionCOEFFICIENTS=-0.415199the coefficients of the arguments in your functionPERIODIC=NO tot_OH-bO:if 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 detailsARG=group_oh_bothe input to this functionCOEFFICIENTS=-0.415199the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
tot:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=group_nh_n,group_nh_o,group_oh_nbo,group_oh_bothe input to this functionCOEFFICIENTS=0.415199,0.415199,-0.415199,-0.415199the coefficients of the arguments in your functionPERIODIC=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_NH-Nthe input for this action is the scalar output from one or more other actionsLABEL=all_NH-Na label for the action so that its output can be referenced in the input to other actionsBIASVALUETakes the value of one variable and use it as a bias More detailsARG=tot_NH-Othe input for this action is the scalar output from one or more other actionsLABEL=all_NH-Oa label for the action so that its output can be referenced in the input to other actionsBIASVALUETakes the value of one variable and use it as a bias More detailsARG=tot_OH-nbOthe input for this action is the scalar output from one or more other actionsLABEL=all_OH-nbOa label for the action so that its output can be referenced in the input to other actionsBIASVALUETakes the value of one variable and use it as a bias More detailsARG=tot_OH-bOthe input for this action is the scalar output from one or more other actionsLABEL=all_OH-bOa label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARG=tot_NH-N,all_NH-N.bias,tot_NH-O,all_NH-O.bias,tot_OH-nbO,all_OH-nbO.bias,tot_OH-bO,all_OH-bO.bias,totthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=check_HBfix.datthe name of the file on which to output these quantities
# eRMSD with augmented cutoff, used for biasing. # The value of the cutoff determines at which distance a pair of nucleobases is counted # as a contact. An augmented value here allows forces to drive # the system towards and away from native even when nucleobases are far from # each other DIST0: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-4,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. 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-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.REFERENCE=GAGA_native.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 calculation
# eRMSD with standard cutoff (2.4), used for monitoring only. # The cutoff employed here is the same used in the original paper # describing the eRMSD metric. This value allows only proper contact to # be included in the assessment of the structures. 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-4,an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. 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-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information.REFERENCE=GAGA_native.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=DIST0the 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=4.5the upper bounds for the gridGRID_SPACING=0.02 # print colvar filethe approximate grid spacing (to be used as an alternative or together with GRID_BIN)Print quantities to a file. More detailsARG=DIST0,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