PLUMED-NEST

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

Click on the labels of the actions for more information on what each action computes

# 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.cpp

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=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis 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=1-293	

# 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_1The GHBFIX action with label group_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
group_1
scalar
the GHBFIX interaction energy between the atoms in GROUPA and GROUPB: GHBFIXCalculate the GHBFIX interaction energy between GROUPA and GROUPB More details PAIR Pair only 1st element of the 1st group with 1st element in the second, etc GROUPAFirst list of atoms=19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,22,22,23,23,19,19,22,22,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,19,19,19,22,22,22,23,23,23,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,55,55,56,56,52,52,55,55,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,52,52,52,55,55,55,56,56,56,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,88,88,89,89,85,85,88,88,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,85,85,85,88,88,88,89,89,89,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,121,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,181,181,181,182,182,182,181,181,181,182,182,182,181,181,181,182,182,182,181,181,182,182,181,181,182,182,181,181,181,182,182,182,181,181,181,182,182,182,181,181,181,182,182,182,214,214,214,217,217,217,218,218,218,214,214,214,217,217,217,218,218,218,214,214,214,217,217,217,218,218,218,214,214,217,217,218,218,214,214,217,217,218,218,214,214,214,217,217,217,218,218,218,214,214,214,217,217,217,218,218,218,214,214,214,217,217,217,218,218,218,247,247,247,250,250,250,251,251,251,247,247,247,250,250,250,251,251,251,247,247,247,250,250,250,251,251,251,247,247,250,250,251,251,247,247,250,250,251,251,247,247,247,250,250,250,251,251,251,247,247,247,250,250,250,251,251,251,247,247,247,250,250,250,251,251,251,280,280,280,283,283,283,284,284,284,280,280,280,283,283,283,284,284,284,280,280,280,283,283,283,284,284,284,280,280,283,283,284,284,280,280,283,283,284,284,280,280,280,283,283,283,284,284,284,280,280,280,283,283,283,284,284,284,280,280,280,283,283,283,284,284,284 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,245,242,252,245,242,252,245,242,252,278,275,285,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,245,242,252,245,242,252,245,242,252,278,275,285,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,245,242,252,245,242,252,245,242,252,278,275,285,278,275,285,278,275,285,17,14,24,50,47,57,83,80,90,151,155,177,183,186,212,209,219,245,242,252,278,275,285,17,14,24,50,47,57,83,80,90,119,123,177,183,186,212,209,219,245,242,252,278,275,285,17,14,24,17,14,24,50,47,57,50,47,57,83,80,90,83,80,90,119,123,119,123,151,155,151,155,212,209,219,212,209,219,245,242,252,245,242,252,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,245,242,252,245,242,252,245,242,252,278,275,285,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,278,275,285,278,275,285,278,275,285,17,14,24,17,14,24,17,14,24,50,47,57,50,47,57,50,47,57,83,80,90,83,80,90,83,80,90,119,123,119,123,119,123,151,155,151,155,151,155,177,183,186,177,183,186,177,183,186,212,209,219,212,209,219,212,209,219,245,242,252,245,242,252,245,242,252 D_0the value of D_0 in the switching function=0.2 D_MAXthe value of D_MAX in the switching function=0.3 Cthe value of C in the switching function=0.8 TYPESthe value of TYPES in the switching function=./gHBfix_typesTable_hairpin.dat PARAMSthe value of PARAMS in the switching function=./gHBfix_scalingParameters_hairpin.dat

# scaling of gHBfix in replicas. reference replica has 2kcal/mol gHBfix. coefs=lambdas (scalingTable has 1.00)
tot_1The COMBINE action with label tot_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
tot_1
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=group_1 COEFFICIENTS the coefficients of the arguments in your function=@replicas:This keyword specifies that different replicas have different values for this quantity.  See here for more details.{2.0000000,1.9092000,1.8225220,1.7397800,1.6607940,1.5853940,1.5134160,1.4447080,1.3791180,1.3165060,1.2567360,1.1996800} 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_1 LABELa label for the action so that its output can be referenced in the input to other actions=all_group_1The BIASVALUE action with label all_group_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
all_group_1.bias
scalar
the instantaneous value of the bias potential
all_group_1.tot_1_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named tot_1

# biasing eRMSD with augmented cutoff:
DISTfullThe ERMSD action with label DISTfull calculates the following quantities:
 Quantity   
 Type   
 Description  
DISTfull
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: 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-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. ,@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=3.2
DISTg5endThe ERMSD action with label DISTg5end calculates the following quantities:
 Quantity   
 Type   
 Description  
DISTg5end
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: 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.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=3.2
DISTg3endThe ERMSD action with label DISTg3end calculates the following quantities:
 Quantity   
 Type   
 Description  
DISTg3end
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. More details ATOMSthe list of atoms (use lcs)=@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. ,@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=3.2

COMBINECalculate a polynomial combination of a set of other variables. More details  LABELa label for the action so that its output can be referenced in the input to other actions=DDThe COMBINE action with label DD calculates the following quantities:
 Quantity   
 Type   
 Description  
DD
scalar
a linear compbination  ARGthe values input to this function=DISTfull,DISTg5end,DISTg3end COEFFICIENTS the coefficients of the arguments in your function=6,-3,-3 POWERS the powers to which you are raising each of the arguments in your function=2,2,2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=interDThe COMBINE action with label interD calculates the following quantities:
 Quantity   
 Type   
 Description  
interD
scalar
a linear compbination  ARGthe values input to this function=DD POWERS the powers to which you are raising each 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 COEFFICIENTS the coefficients of the arguments in your function=0.40824829 #COEF=sqrt(1/6)

# eRMSD with standard cutoff (2.4), used for monitoring only:
DIST1The ERMSD action with label DIST1 calculates the following quantities:
 Quantity   
 Type   
 Description  
DIST1
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: 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-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. ,@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb
DIST1: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. 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-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. ,@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb  CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4

# metadynamics
metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=interD 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=4.0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.02

# print 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=tot_1,all_group_1.bias STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=check_ghbfix.dat
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=interD,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