PLUMED-NEST

Project ID: plumID:21.016
Source: input_files/plumed.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

#SETTINGS NATOMS=168751
# 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=hrex_total_renum.pdb

The MOLINFO action with label  calculates somethingn: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-1833
The GROUP action with label n calculates somethingh: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=@hydrogensall hydrogen atoms. Click here for more information. 
The GROUP action with label h calculates somethingnnh: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=n REMOVEremove these atoms from the list=h

The GROUP action with label nnh 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=nnh

# Rg, Diff
Rg: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=nnh

The GYRATION action with label Rg calculates the following quantities:
 Quantity   
 Description  
Rg.value
the radius that was computed from the weightsfull: 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=npt_no_contact.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-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-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. 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. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. ,@lcs-17an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. Click here for more information. ,@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-21an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. ,@lcs-22an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. ,@lcs-23an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. ,@lcs-24an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. ,@lcs-25an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. 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. ,@lcs-29an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. 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. ,@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. ,@lcs-36an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. 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. ,@lcs-45an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 45. Click here for more information. ,@lcs-46an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 46. Click here for more information. ,@lcs-47an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. ,@lcs-48an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. ,@lcs-49an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. ,@lcs-50an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information. ,@lcs-51an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 51. Click here for more information. ,@lcs-52an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information. ,@lcs-53an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information. ,@lcs-54an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information. ,@lcs-55an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information. ,@lcs-56an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information. ,@lcs-57an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information. 
The ERMSD action with label full calculates the following quantities:
 Quantity   
 Description  
full.value
the eRMSD between the instantaneous structure and the reference structure that was inputstem1: 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=npt_no_contact.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-52an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information. ,@lcs-53an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information. ,@lcs-54an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information. ,@lcs-55an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information. ,@lcs-56an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information. ,@lcs-57an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information. 
The ERMSD action with label stem1 calculates the following quantities:
 Quantity   
 Description  
stem1.value
the eRMSD between the instantaneous structure and the reference structure that was inputstem2: 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=npt_no_contact.pdb ATOMSthe list of atoms (use lcs)=@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-28an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. ,@lcs-29an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. 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. 
The ERMSD action with label stem2 calculates the following quantities:
 Quantity   
 Description  
stem2.value
the eRMSD between the instantaneous structure and the reference structure that was inputstem3: 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=npt_no_contact.pdb ATOMSthe list of atoms (use lcs)=@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. 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-22an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. ,@lcs-23an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. ,@lcs-24an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. ,@lcs-25an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. 
The ERMSD action with label stem3 calculates the following quantities:
 Quantity   
 Description  
stem3.value
the eRMSD between the instantaneous structure and the reference structure that was inputstem4: 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=npt_no_contact.pdb ATOMSthe list of atoms (use lcs)=@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-47an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. ,@lcs-48an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. ,@lcs-49an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. ,@lcs-50an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information. 

The ERMSD action with label stem4 calculates the following quantities:
 Quantity   
 Description  
stem4.value
the eRMSD between the instantaneous structure and the reference structure that was inputdiff: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=full,stem1,stem2,stem3,stem4 VARthe names to give each of the arguments in the function=full,stem1,stem2,stem3,stem4 FUNCthe function you wish to evaluate=sqrt(57*full^2-11*stem1^2-6*stem2^2-8*stem3^2-8*stem4^2) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# eRMSD on the whole structure and stems
The CUSTOM action with label diff calculates the following quantities:
 Quantity   
 Description  
diff.value
an arbitrary functionfullx: 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=npt_solute.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-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-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. 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. ,@lcs-16an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. ,@lcs-17an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. Click here for more information. ,@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-21an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. ,@lcs-22an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. ,@lcs-23an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. ,@lcs-24an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. ,@lcs-25an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. 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. ,@lcs-29an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. 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. ,@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. ,@lcs-36an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. 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. ,@lcs-45an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 45. Click here for more information. ,@lcs-46an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 46. Click here for more information. ,@lcs-47an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. ,@lcs-48an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. ,@lcs-49an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. ,@lcs-50an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information. ,@lcs-51an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 51. Click here for more information. ,@lcs-52an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information. ,@lcs-53an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information. ,@lcs-54an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information. ,@lcs-55an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information. ,@lcs-56an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information. ,@lcs-57an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information. 
The ERMSD action with label fullx calculates the following quantities:
 Quantity   
 Description  
fullx.value
the eRMSD between the instantaneous structure and the reference structure that was inputstem1x: 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=npt_solute.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-52an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information. ,@lcs-53an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information. ,@lcs-54an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information. ,@lcs-55an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information. ,@lcs-56an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information. ,@lcs-57an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information. 
The ERMSD action with label stem1x calculates the following quantities:
 Quantity   
 Description  
stem1x.value
the eRMSD between the instantaneous structure and the reference structure that was inputstem2x: 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=npt_solute.pdb ATOMSthe list of atoms (use lcs)=@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-28an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. ,@lcs-29an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. 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. 
The ERMSD action with label stem2x calculates the following quantities:
 Quantity   
 Description  
stem2x.value
the eRMSD between the instantaneous structure and the reference structure that was inputstem3x: 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=npt_solute.pdb ATOMSthe list of atoms (use lcs)=@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. 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-22an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. ,@lcs-23an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. ,@lcs-24an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. ,@lcs-25an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. 
The ERMSD action with label stem3x calculates the following quantities:
 Quantity   
 Description  
stem3x.value
the eRMSD between the instantaneous structure and the reference structure that was inputstem4x: 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=npt_solute.pdb ATOMSthe list of atoms (use lcs)=@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-47an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. ,@lcs-48an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. ,@lcs-49an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. ,@lcs-50an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information. 


# SAXS computation and Ratio CV
The ERMSD action with label stem4x calculates the following quantities:
 Quantity   
 Description  
stem4x.value
the eRMSD between the instantaneous structure and the reference structure that was inputINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=cg_map.dat

SAXSCalculates SAXS intensity. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=saxs
ATOMSThe atoms to be included in the calculation, e=martini
MARTINI Calculate SAXS for a Martini model

NOPBC Ignore the periodic boundary conditions when calculating distances

SCALEINT=1
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.001
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.025
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.05
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.075
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.25
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.35
... SAXS

The SAXS action with label saxs calculates the following quantities:
 Quantity   
 Description  
saxs.score
the Metainference score
saxs.sigma
uncertainty parameter
saxs.sigmaMean
uncertainty in the mean estimate
saxs.neff
effective number of replicas
saxs.acceptSigma
MC acceptance for sigma values
saxs.q
The # SAXS of qSAXSCalculates SAXS intensity. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=saxs_bias

ATOMSThe atoms to be included in the calculation, e=martini
MARTINI Calculate SAXS for a Martini model

NOPBC Ignore the periodic boundary conditions when calculating distances

SCALEINT=1
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2
... SAXS

The SAXS action with label saxs_bias calculates the following quantities:
 Quantity   
 Description  
saxs_bias.score
the Metainference score
saxs_bias.sigma
uncertainty parameter
saxs_bias.sigmaMean
uncertainty in the mean estimate
saxs_bias.neff
effective number of replicas
saxs_bias.acceptSigma
MC acceptance for sigma values
saxs_bias.q
The # SAXS of qratio: CUSTOMCalculate a combination of variables using a custom expression. More details FUNCthe function you wish to evaluate=(a*0.01)/(b*0.04) ARGthe values input to this function=saxs_bias.q-0,saxs_bias.q-1 VARthe names to give each of the arguments in the function=a,b PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# walls on the stems, on Rg and on Ratio
The CUSTOM action with label ratio calculates the following quantities:
 Quantity   
 Description  
ratio.value
an arbitrary functionuwall1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=stem1x ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=41.84 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=0.3
The UPPER_WALLS action with label uwall1 calculates the following quantities:
 Quantity   
 Description  
uwall1.bias
the instantaneous value of the bias potential
uwall1.force2
the instantaneous value of the squared force due to this bias potentialuwall2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=stem2x ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=41.84 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=0.3
The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Description  
uwall2.bias
the instantaneous value of the bias potential
uwall2.force2
the instantaneous value of the squared force due to this bias potentialuwall3: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=stem3x ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=41.84 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=0.3
The UPPER_WALLS action with label uwall3 calculates the following quantities:
 Quantity   
 Description  
uwall3.bias
the instantaneous value of the bias potential
uwall3.force2
the instantaneous value of the squared force due to this bias potentialuwall4: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=stem4x ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=41.84 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=0.3

The UPPER_WALLS action with label uwall4 calculates the following quantities:
 Quantity   
 Description  
uwall4.bias
the instantaneous value of the bias potential
uwall4.force2
the instantaneous value of the squared force due to this bias potentiallwall:  LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=Rg ATthe positions of the wall=1.60 KAPPAthe force constant for the wall=41.84 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=0.01
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialuwall:  UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=Rg ATthe positions of the wall=2.5  KAPPAthe force constant for the wall=41.84 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=0.01

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialuwall_ratio:  UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=ratio ATthe positions of the wall=2.7  KAPPAthe force constant for the wall=41.84 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=0.01

# metadynamics
The UPPER_WALLS action with label uwall_ratio calculates the following quantities:
 Quantity   
 Description  
uwall_ratio.bias
the instantaneous value of the bias potential
uwall_ratio.force2
the instantaneous value of the squared force due to this bias potentialmeta: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=ratio,diff SIGMAthe widths of the Gaussian hills=0.035,0.05 HEIGHTthe heights of the Gaussian hills=2.09 BIASFACTORuse well tempered metadynamics and use this bias factor=10 PACEthe frequency for hill addition=400 GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=8,14 STRIDEthe frequency with which the forces due to the bias should be calculated=2

# print stuff
The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxs\.q-.*),ratio FILEthe name of the file on which to output these quantities=colvar_check_saxs STRIDE the frequency with which the quantities of interest should be output=5000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=Rg,ratio,diff,full,(stem.),(.*x),meta.bias,(uwall.\.bias),lwall.bias,uwall.bias,uwall_ratio.bias FILEthe name of the file on which to output these quantities=COLVAR_metad STRIDE the frequency with which the quantities of interest should be output=100