Project ID: plumID:21.051
Source: plumed-nest/ST-MetaD/GAGA_gHBfix_1-0/plumed.0.dat
Originally used with PLUMED version: 2.5
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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. # choose units - by default PLUMED uses kj/mol, nm, and ps # UNITS ENERGY=kcal/mol LENGTH=A
# 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 details STRUCTUREa file in pdb format containing a reference structure=GAGA_native.pdb WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-263 #################################################################################################### # gHBfix RESTRAINT SECTION ####################################################################################################
group_nh_n: COORDINATIONCalculate coordination numbers. More details PAIR Pair only 1st element of the 1st group with 1st element in the second, etc GROUPAFirst list of atoms=19,22,23,19,19,22,22,23,23,19,19,19,22,22,22,23,23,23,19,19,22,22,23,23,19,19,19,22,22,22,23,23,23,19,19,22,22,23,23,19,22,23,52,52,53,53,52,52,53,53,52,52,52,53,53,53,52,52,53,53,52,52,52,53,53,53,52,52,53,53,52,53,84,84,87,87,88,88,84,87,88,84,84,84,87,87,87,88,88,88,84,84,87,87,88,88,84,84,84,87,87,87,88,88,88,84,84,87,87,88,88,84,87,88,117,117,118,118,117,118,117,117,118,118,117,117,118,118,117,117,117,118,118,118,117,117,118,118,117,118,151,151,154,154,155,155,151,154,155,151,151,154,154,155,155,151,151,151,154,154,154,155,155,155,151,151,151,154,154,154,155,155,155,151,151,154,154,155,155,151,154,155,184,184,185,185,184,185,184,184,185,185,184,184,184,185,185,185,184,184,185,185,184,184,185,185,184,185,218,218,221,221,222,222,218,221,222,218,218,221,221,222,222,218,218,218,221,221,221,222,222,222,218,218,221,221,222,222,218,218,218,221,221,221,222,222,222,218,221,222,251,251,252,252,251,252,251,251,252,252,251,251,251,252,252,252,251,251,252,252,251,251,251,252,252,252,251,251,252,252 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=54,54,54,79,89,79,89,79,89,113,119,122,113,119,122,113,119,122,146,156,146,156,146,156,180,186,189,180,186,189,180,186,189,213,223,213,223,213,223,253,253,253,14,24,14,24,79,89,79,89,113,119,122,113,119,122,146,156,146,156,180,186,189,180,186,189,213,223,213,223,253,253,14,24,14,24,14,24,54,54,54,113,119,122,113,119,122,113,119,122,146,156,146,156,146,156,180,186,189,180,186,189,180,186,189,213,223,213,223,213,223,253,253,253,14,24,14,24,54,54,79,89,79,89,146,156,146,156,180,186,189,180,186,189,213,223,213,223,253,253,14,24,14,24,14,24,54,54,54,79,89,79,89,79,89,113,119,122,113,119,122,113,119,122,180,186,189,180,186,189,180,186,189,213,223,213,223,213,223,253,253,253,14,24,14,24,54,54,79,89,79,89,113,119,122,113,119,122,146,156,146,156,213,223,213,223,253,253,14,24,14,24,14,24,54,54,54,79,89,79,89,79,89,113,119,122,113,119,122,113,119,122,146,156,146,156,146,156,180,186,189,180,186,189,180,186,189,253,253,253,14,24,14,24,54,54,79,89,79,89,113,119,122,113,119,122,146,156,146,156,180,186,189,180,186,189,213,223,213,223 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={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}
group_oh_nbo: COORDINATIONCalculate coordination numbers. More details PAIR Pair only 1st element of the 1st group with 1st element in the second, etc GROUPAFirst list of atoms=31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,62,62,62,62,62,62,62,62,62,62,62,62,62,62,96,96,96,96,96,96,96,96,96,96,96,96,96,96,129,129,129,129,129,129,129,129,129,129,129,129,129,129,163,163,163,163,163,163,163,163,163,163,163,163,163,163,196,196,196,196,196,196,196,196,196,196,196,196,196,196,230,230,230,230,230,230,230,230,230,230,230,230,230,230,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=34,35,34,35,65,66,65,66,99,100,99,100,132,133,132,133,166,167,166,167,199,200,199,200,233,234,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,34,35,65,66,65,66,99,100,99,100,132,133,132,133,166,167,166,167,199,200,199,200,233,234,233,234 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={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}
group_oh_bo: COORDINATIONCalculate coordination numbers. More details PAIR Pair only 1st element of the 1st group with 1st element in the second, etc GROUPAFirst list of atoms=1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,1,62,62,62,62,62,62,62,62,62,62,62,62,62,96,96,96,96,96,96,96,96,96,96,96,96,96,129,129,129,129,129,129,129,129,129,129,129,129,129,163,163,163,163,163,163,163,163,163,163,163,163,163,196,196,196,196,196,196,196,196,196,196,196,196,196,230,230,230,230,230,230,230,230,230,230,230,230,230,261,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,263 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=32,36,63,36,63,67,97,67,97,101,130,101,130,134,164,134,164,168,197,168,197,201,231,201,231,235,235,32,36,67,97,101,130,134,164,168,197,201,231,235,32,36,63,67,101,130,134,164,168,197,201,231,235,32,36,63,67,97,101,134,164,168,197,201,231,235,32,36,63,67,97,101,130,134,168,197,201,231,235,32,36,63,67,97,101,130,134,164,168,201,231,235,32,36,63,67,97,101,130,134,164,168,197,201,235,32,32,36,63,36,63,67,97,67,97,101,130,101,130,134,164,134,164,168,197,168,197,201,231,201,231,235,235 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={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}
tot_NH-N: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=group_nh_n COEFFICIENTS the coefficients of the arguments in your function=1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO tot_OH-nbO: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=group_oh_nbo COEFFICIENTS the coefficients of the arguments in your function=-0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO tot_OH-bO: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=group_oh_bo COEFFICIENTS the coefficients of the arguments in your function=-0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO tot: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=group_nh_n,group_oh_nbo,group_oh_bo COEFFICIENTS the coefficients of the arguments in your function=1,-0.5,-0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=tot_NH-N LABELa label for the action so that its output can be referenced in the input to other actions=all_NH-N BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=tot_OH-nbO LABELa label for the action so that its output can be referenced in the input to other actions=all_OH-nbO BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=tot_OH-bO LABELa label for the action so that its output can be referenced in the input to other actions=all_OH-bO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=tot_NH-N,all_NH-N.bias,tot_OH-nbO,all_OH-nbO.bias,tot_OH-bO,all_OH-bO.bias,tot STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=check_HBfix.dat # 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 details ATOMSthe list of atoms (use lcs)=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. ,@lcs-2an 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. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an 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. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_native.pdb CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=3.2 # 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. This action has hidden defaults. More details ATOMSthe list of atoms (use lcs)=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. ,@lcs-2an 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. ,@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. ,@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. ,@lcs-6an 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. ,@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=GAGA_native.pdb
# metadynamics metad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=DIST0 PACEthe frequency for hill addition=250 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=70 SIGMAthe widths of the Gaussian hills=0.1 FILE a file in which the list of added hills is stored=HILLS TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 BIASFACTORuse well tempered metadynamics and use this bias factor=15 GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=4.5 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.02 # print colvar file PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=DIST0,DIST1,metad.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=250