PLUMED-NEST

Project ID: plumID:23.033
Source: plumed_inputs/G4_full_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. 

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/G4/G4_full.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=1-491	

# biasing eRMSD:
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-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-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. ,@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. ,@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/G4/G4_full.pdb CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=3.2
DISTpart1The ERMSD action with label DISTpart1 calculates the following quantities:
 Quantity   
 Type   
 Description  
DISTpart1
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/G4/G4_full.pdb CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=3.2
DISTpart2The ERMSD action with label DISTpart2 calculates the following quantities:
 Quantity   
 Type   
 Description  
DISTpart2
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-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.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/G4/G4_full.pdb CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=3.2
DISTpart3The ERMSD action with label DISTpart3 calculates the following quantities:
 Quantity   
 Type   
 Description  
DISTpart3
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-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/G4/G4_full.pdb CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=3.2
DISTpart4The ERMSD action with label DISTpart4 calculates the following quantities:
 Quantity   
 Type   
 Description  
DISTpart4
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-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. ,@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. ,@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/G4/G4_full.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,DISTpart1,DISTpart2,DISTpart3,DISTpart4 COEFFICIENTS the coefficients of the arguments in your function=12,-3,-3,-3,-3 POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2 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=0.288675135  #COEF=sqrt(1/12)

# 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-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-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. ,@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. ,@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/G4/G4_full.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-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-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. ,@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. ,@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information.  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../reference_structures/G4/G4_full.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=5.0 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=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