PLUMED-NEST by plumed-nest

Project ID: plumID:20.034
Source: plumed_SL4.dat
Originally used with PLUMED version: 2.5.3
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
RESTARTActivate restart. More details
The RESTART action with label  calculates somethingMOLINFOThis 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=SL4_ext_gmx.pdb MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=rna

# calculate eRMSD for each helical template
ermsd0_p1The ERMSD action with label ermsd0_p1 calculates the following quantities: Quantity    Type    Description  
ermsd0_p1 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 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p1.pdb 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. ,@lcs-37an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. ,@lcs-38an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. ,@lcs-39an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. ,@lcs-40an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. ,@lcs-41an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. ,@lcs-42an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information. ,@lcs-43an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 43. Click here for more information. ,@lcs-44an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 44. Click here for more information. 
ermsd0_p1: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p1.pdb 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. ,@lcs-37an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. ,@lcs-38an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. ,@lcs-39an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. ,@lcs-40an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. ,@lcs-41an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. ,@lcs-42an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information. ,@lcs-43an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 43. Click here for more information. ,@lcs-44an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 44. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
ermsd1_p1The ERMSD action with label ermsd1_p1 calculates the following quantities: Quantity    Type    Description  
ermsd1_p1 scalar the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p1.pdb 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. ,@lcs-37an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. ,@lcs-38an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. ,@lcs-39an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. ,@lcs-40an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. ,@lcs-41an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. ,@lcs-42an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information. ,@lcs-43an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 43. Click here for more information. ,@lcs-44an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 44. Click here for more information.  CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=12

ermsd0_p2The ERMSD action with label ermsd0_p2 calculates the following quantities: Quantity    Type    Description  
ermsd0_p2 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 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p2.pdb ATOMSthe list of atoms (use lcs)=@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-34an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. ,@lcs-35an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information. 
ermsd0_p2: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p2.pdb ATOMSthe list of atoms (use lcs)=@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-34an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. ,@lcs-35an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
ermsd1_p2The ERMSD action with label ermsd1_p2 calculates the following quantities: Quantity    Type    Description  
ermsd1_p2 scalar the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p2.pdb ATOMSthe list of atoms (use lcs)=@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-34an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. ,@lcs-35an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information.  CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=12

ermsd0_p3The ERMSD action with label ermsd0_p3 calculates the following quantities: Quantity    Type    Description  
ermsd0_p3 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 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p3.pdb 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. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. ,@lcs-30an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. ,@lcs-31an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. ,@lcs-32an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. ,@lcs-33an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information. 
ermsd0_p3: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p3.pdb 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. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. ,@lcs-30an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. ,@lcs-31an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. ,@lcs-32an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. ,@lcs-33an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
ermsd1_p3The ERMSD action with label ermsd1_p3 calculates the following quantities: Quantity    Type    Description  
ermsd1_p3 scalar the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p3.pdb 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. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. ,@lcs-30an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. ,@lcs-31an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. ,@lcs-32an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. ,@lcs-33an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information.  CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=12

ermsd0_p4The ERMSD action with label ermsd0_p4 calculates the following quantities: Quantity    Type    Description  
ermsd0_p4 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 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p4.pdb ATOMSthe list of atoms (use lcs)=@lcs-18an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. ,@lcs-19an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. ,@lcs-20an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. ,@lcs-26an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. ,@lcs-27an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. ,@lcs-28an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. 
ermsd0_p4: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p4.pdb ATOMSthe list of atoms (use lcs)=@lcs-18an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. ,@lcs-19an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. ,@lcs-20an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. ,@lcs-26an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. ,@lcs-27an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. ,@lcs-28an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
ermsd1_p4The ERMSD action with label ermsd1_p4 calculates the following quantities: Quantity    Type    Description  
ermsd1_p4 scalar the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL4_target_p4.pdb ATOMSthe list of atoms (use lcs)=@lcs-18an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. ,@lcs-19an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. ,@lcs-20an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. ,@lcs-26an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. ,@lcs-27an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. ,@lcs-28an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information.  CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=12

# print the distance between different bases 
c1The CENTER_FAST action with label c1 calculates the following quantities: Quantity    Type    Description  
c1 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
c2The CENTER_FAST action with label c2 calculates the following quantities: Quantity    Type    Description  
c2 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
c3The CENTER_FAST action with label c3 calculates the following quantities: Quantity    Type    Description  
c3 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
c4The CENTER_FAST action with label c4 calculates the following quantities: Quantity    Type    Description  
c4 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
c5The CENTER_FAST action with label c5 calculates the following quantities: Quantity    Type    Description  
c5 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
c6The CENTER_FAST action with label c6 calculates the following quantities: Quantity    Type    Description  
c6 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
c7The CENTER_FAST action with label c7 calculates the following quantities: Quantity    Type    Description  
c7 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
c8The CENTER_FAST action with label c8 calculates the following quantities: Quantity    Type    Description  
c8 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 

c10The CENTER_FAST action with label c10 calculates the following quantities: Quantity    Type    Description  
c10 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. 
c11The CENTER_FAST action with label c11 calculates the following quantities: Quantity    Type    Description  
c11 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 

c13The CENTER_FAST action with label c13 calculates the following quantities: Quantity    Type    Description  
c13 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
c14The CENTER_FAST action with label c14 calculates the following quantities: Quantity    Type    Description  
c14 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
c15The CENTER_FAST action with label c15 calculates the following quantities: Quantity    Type    Description  
c15 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. 
c16The CENTER_FAST action with label c16 calculates the following quantities: Quantity    Type    Description  
c16 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. 

c18The CENTER_FAST action with label c18 calculates the following quantities: Quantity    Type    Description  
c18 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-18an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. 
c19The CENTER_FAST action with label c19 calculates the following quantities: Quantity    Type    Description  
c19 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-19an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. 
c20The CENTER_FAST action with label c20 calculates the following quantities: Quantity    Type    Description  
c20 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-20an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. 

c26The CENTER_FAST action with label c26 calculates the following quantities: Quantity    Type    Description  
c26 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-26an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. 
c27The CENTER_FAST action with label c27 calculates the following quantities: Quantity    Type    Description  
c27 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-27an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. 
c28The CENTER_FAST action with label c28 calculates the following quantities: Quantity    Type    Description  
c28 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-28an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. 

c30The CENTER_FAST action with label c30 calculates the following quantities: Quantity    Type    Description  
c30 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-30an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. 
c31The CENTER_FAST action with label c31 calculates the following quantities: Quantity    Type    Description  
c31 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-31an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. 
c32The CENTER_FAST action with label c32 calculates the following quantities: Quantity    Type    Description  
c32 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-32an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. 
c33The CENTER_FAST action with label c33 calculates the following quantities: Quantity    Type    Description  
c33 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-33an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information. 

c34The CENTER_FAST action with label c34 calculates the following quantities: Quantity    Type    Description  
c34 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-34an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. 
c35The CENTER_FAST action with label c35 calculates the following quantities: Quantity    Type    Description  
c35 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-35an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information. 


c37The CENTER_FAST action with label c37 calculates the following quantities: Quantity    Type    Description  
c37 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-37an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. 
c38The CENTER_FAST action with label c38 calculates the following quantities: Quantity    Type    Description  
c38 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-38an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. 
c39The CENTER_FAST action with label c39 calculates the following quantities: Quantity    Type    Description  
c39 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-39an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. 
c40The CENTER_FAST action with label c40 calculates the following quantities: Quantity    Type    Description  
c40 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-40an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. 
c41The CENTER_FAST action with label c41 calculates the following quantities: Quantity    Type    Description  
c41 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-41an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. 
c42The CENTER_FAST action with label c42 calculates the following quantities: Quantity    Type    Description  
c42 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-42an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information. 
c43The CENTER_FAST action with label c43 calculates the following quantities: Quantity    Type    Description  
c43 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-43an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 43. Click here for more information. 
c44The CENTER_FAST action with label c44 calculates the following quantities: Quantity    Type    Description  
c44 atoms virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-44an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 44. Click here for more information. 


dp1_1The DISTANCE action with label dp1_1 calculates the following quantities: Quantity    Type    Description  
dp1_1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c44
dp1_2The DISTANCE action with label dp1_2 calculates the following quantities: Quantity    Type    Description  
dp1_2 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c2,c43
dp1_3The DISTANCE action with label dp1_3 calculates the following quantities: Quantity    Type    Description  
dp1_3 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c3,c42
dp1_4The DISTANCE action with label dp1_4 calculates the following quantities: Quantity    Type    Description  
dp1_4 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c4,c41
dp1_5The DISTANCE action with label dp1_5 calculates the following quantities: Quantity    Type    Description  
dp1_5 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c5,c40
dp1_6The DISTANCE action with label dp1_6 calculates the following quantities: Quantity    Type    Description  
dp1_6 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c6,c39
dp1_7The DISTANCE action with label dp1_7 calculates the following quantities: Quantity    Type    Description  
dp1_7 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c7,c38
dp1_8The DISTANCE action with label dp1_8 calculates the following quantities: Quantity    Type    Description  
dp1_8 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c8,c37

dp2_1The DISTANCE action with label dp2_1 calculates the following quantities: Quantity    Type    Description  
dp2_1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c10,c35
dp2_2The DISTANCE action with label dp2_2 calculates the following quantities: Quantity    Type    Description  
dp2_2 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c11,c34

dp3_1The DISTANCE action with label dp3_1 calculates the following quantities: Quantity    Type    Description  
dp3_1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c13,c33
dp3_2The DISTANCE action with label dp3_2 calculates the following quantities: Quantity    Type    Description  
dp3_2 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c14,c32
dp3_3The DISTANCE action with label dp3_3 calculates the following quantities: Quantity    Type    Description  
dp3_3 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c15,c31
dp3_4The DISTANCE action with label dp3_4 calculates the following quantities: Quantity    Type    Description  
dp3_4 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c16,c30

dp4_1The DISTANCE action with label dp4_1 calculates the following quantities: Quantity    Type    Description  
dp4_1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c18,c28
dp4_2The DISTANCE action with label dp4_2 calculates the following quantities: Quantity    Type    Description  
dp4_2 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c19,c27
dp4_3The DISTANCE action with label dp4_3 calculates the following quantities: Quantity    Type    Description  
dp4_3 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c20,c26


# here we instatiate 4 different ABMD. This is identical to one ABMD with 4 arguments,
# with the only difference that we can print the bias of each spring individually
ABMDAdds a ratchet-and-pawl like restraint on one or more variables. More details ... 
ARGthe labels of the scalars on which the bias will act=ermsd1_p1
KAPPAThe array of force constants=4
TOThe array of target values=1
LABELa label for the action so that its output can be referenced in the input to other actions=qq1The ABMD action with label qq1 calculates the following quantities: Quantity    Type    Description  
qq1.bias scalar the instantaneous value of the bias potential
qq1.ermsd1_p1_min scalar one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named ermsd1_p1
qq1.force2 scalar the instantaneous value of the squared force due to this bias potential 
... ABMD

ABMDAdds a ratchet-and-pawl like restraint on one or more variables. More details ... 
ARGthe labels of the scalars on which the bias will act=ermsd1_p2
KAPPAThe array of force constants=4
TOThe array of target values=1
LABELa label for the action so that its output can be referenced in the input to other actions=qq2The ABMD action with label qq2 calculates the following quantities: Quantity    Type    Description  
qq2.bias scalar the instantaneous value of the bias potential
qq2.ermsd1_p2_min scalar one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named ermsd1_p2
qq2.force2 scalar the instantaneous value of the squared force due to this bias potential
... ABMD

ABMDAdds a ratchet-and-pawl like restraint on one or more variables. More details ... 
ARGthe labels of the scalars on which the bias will act=ermsd1_p3
KAPPAThe array of force constants=4
TOThe array of target values=1
LABELa label for the action so that its output can be referenced in the input to other actions=qq3The ABMD action with label qq3 calculates the following quantities: Quantity    Type    Description  
qq3.bias scalar the instantaneous value of the bias potential
qq3.ermsd1_p3_min scalar one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named ermsd1_p3
qq3.force2 scalar the instantaneous value of the squared force due to this bias potential 
... ABMD

ABMDAdds a ratchet-and-pawl like restraint on one or more variables. More details ... 
ARGthe labels of the scalars on which the bias will act=ermsd1_p4
KAPPAThe array of force constants=4
TOThe array of target values=1
LABELa label for the action so that its output can be referenced in the input to other actions=qq4The ABMD action with label qq4 calculates the following quantities: Quantity    Type    Description  
qq4.bias scalar the instantaneous value of the bias potential
qq4.ermsd1_p4_min scalar one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named ermsd1_p4
qq4.force2 scalar the instantaneous value of the squared force due to this bias potential 
... ABMD

PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=Q_YYY ARGthe labels of the values that you would like to print to the file=qq1.bias,qq2.bias,qq3.bias,qq4.bias STRIDE the frequency with which the quantities of interest should be output=5000
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=ERMSD_YYY ARGthe labels of the values that you would like to print to the file=ermsd0_p1,ermsd0_p2,ermsd0_p3,ermsd0_p4,ermsd1_p1,ermsd1_p2,ermsd1_p3,ermsd1_p4 STRIDE the frequency with which the quantities of interest should be output=5000
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=DIST_YYY ARGthe labels of the values that you would like to print to the file=dp1_1,dp1_2,dp1_3,dp1_4,dp1_5,dp1_6,dp1_7,dp1_8,dp2_1,dp2_2,dp3_1,dp3_2,dp3_3,dp3_4,dp4_1,dp4_2 STRIDE the frequency with which the quantities of interest should be output=5000
Quantity	Type	Description
ermsd0_p1	scalar	the eRMSD between the instantaneous structure and the reference structure that was input
PLUMED-NEST

The public repository of the PLUMED consortium
