Project ID: plumID:23.033
Source: plumed_inputs/parallel_hairpin_intertract_eRMSD_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.MOLINFOThis 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
# biasing eRMSD: 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 colvar filePrint 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