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
tested onv2.9
tested onmaster
#SETTINGS NATOMS=168751

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 


MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=hrex_total_renum.pdb

n: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-1833
h: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=
@hydrogens
all hydrogen atoms. Click here for more information. 

nnh: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=n 
REMOVE
remove these atoms from the list
=h

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=nnh

# Rg, Diff
Rg: 
GYRATION
Calculate 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 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=nnh

full: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_no_contact.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
,
@lcs-10
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. 
,
@lcs-11
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 
,
@lcs-12
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 
,
@lcs-13
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
,
@lcs-14
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
,
@lcs-15
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. 
,
@lcs-16
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. 
,
@lcs-17
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. Click here for more information. 
,
@lcs-18
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. 
,
@lcs-19
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. 
,
@lcs-20
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. 
,
@lcs-21
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. 
,
@lcs-22
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. 
,
@lcs-23
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. 
,
@lcs-24
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. 
,
@lcs-25
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. 
,
@lcs-26
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. 
,
@lcs-27
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. 
,
@lcs-28
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. 
,
@lcs-29
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information. 
,
@lcs-30
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. 
,
@lcs-31
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. 
,
@lcs-32
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. 
,
@lcs-33
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information. 
,
@lcs-34
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. 
,
@lcs-35
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information. 
,
@lcs-36
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. Click here for more information. 
,
@lcs-37
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. 
,
@lcs-38
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. 
,
@lcs-39
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. 
,
@lcs-40
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. 
,
@lcs-41
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. 
,
@lcs-42
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information. 
,
@lcs-43
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 43. Click here for more information. 
,
@lcs-44
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 44. Click here for more information. 
,
@lcs-45
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 45. Click here for more information. 
,
@lcs-46
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 46. Click here for more information. 
,
@lcs-47
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. 
,
@lcs-48
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. 
,
@lcs-49
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. 
,
@lcs-50
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information. 
,
@lcs-51
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 51. Click here for more information. 
,
@lcs-52
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information. 
,
@lcs-53
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information. 
,
@lcs-54
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information. 
,
@lcs-55
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information. 
,
@lcs-56
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information. 
,
@lcs-57
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information. 

stem1: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_no_contact.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-52
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information. 
,
@lcs-53
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information. 
,
@lcs-54
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information. 
,
@lcs-55
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information. 
,
@lcs-56
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information. 
,
@lcs-57
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information. 

stem2: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_no_contact.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-28
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. 
,
@lcs-29
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information. 
,
@lcs-30
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. 

stem3: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_no_contact.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-11
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 
,
@lcs-12
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 
,
@lcs-13
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
,
@lcs-14
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
,
@lcs-22
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. 
,
@lcs-23
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. 
,
@lcs-24
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. 
,
@lcs-25
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. 

stem4: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_no_contact.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-39
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. 
,
@lcs-40
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. 
,
@lcs-41
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. 
,
@lcs-42
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information. 
,
@lcs-47
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. 
,
@lcs-48
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. 
,
@lcs-49
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. 
,
@lcs-50
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information. 


diff: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=full,stem1,stem2,stem3,stem4 
VAR
the names to give each of the arguments in the function
=full,stem1,stem2,stem3,stem4 
FUNC
the function you wish to evaluate
=sqrt(57*full^2-11*stem1^2-6*stem2^2-8*stem3^2-8*stem4^2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# eRMSD on the whole structure and stems
fullx: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_solute.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
,
@lcs-10
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. 
,
@lcs-11
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 
,
@lcs-12
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 
,
@lcs-13
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
,
@lcs-14
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
,
@lcs-15
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. 
,
@lcs-16
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. 
,
@lcs-17
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. Click here for more information. 
,
@lcs-18
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. 
,
@lcs-19
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. 
,
@lcs-20
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. 
,
@lcs-21
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. 
,
@lcs-22
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. 
,
@lcs-23
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. 
,
@lcs-24
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. 
,
@lcs-25
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. 
,
@lcs-26
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. 
,
@lcs-27
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. 
,
@lcs-28
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. 
,
@lcs-29
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information. 
,
@lcs-30
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. 
,
@lcs-31
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. 
,
@lcs-32
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. 
,
@lcs-33
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information. 
,
@lcs-34
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. 
,
@lcs-35
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information. 
,
@lcs-36
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 36. Click here for more information. 
,
@lcs-37
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. 
,
@lcs-38
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. 
,
@lcs-39
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. 
,
@lcs-40
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. 
,
@lcs-41
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. 
,
@lcs-42
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information. 
,
@lcs-43
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 43. Click here for more information. 
,
@lcs-44
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 44. Click here for more information. 
,
@lcs-45
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 45. Click here for more information. 
,
@lcs-46
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 46. Click here for more information. 
,
@lcs-47
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. 
,
@lcs-48
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. 
,
@lcs-49
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. 
,
@lcs-50
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 50. Click here for more information. 
,
@lcs-51
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 51. Click here for more information. 
,
@lcs-52
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information. 
,
@lcs-53
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information. 
,
@lcs-54
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information. 
,
@lcs-55
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information. 
,
@lcs-56
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information. 
,
@lcs-57
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information. 

stem1x: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_solute.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-52
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 52. Click here for more information. 
,
@lcs-53
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 53. Click here for more information. 
,
@lcs-54
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 54. Click here for more information. 
,
@lcs-55
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 55. Click here for more information. 
,
@lcs-56
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 56. Click here for more information. 
,
@lcs-57
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 57. Click here for more information. 

stem2x: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_solute.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-28
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. 
,
@lcs-29
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information. 
,
@lcs-30
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. 

stem3x: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_solute.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-11
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 
,
@lcs-12
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 
,
@lcs-13
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
,
@lcs-14
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
,
@lcs-22
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. 
,
@lcs-23
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. 
,
@lcs-24
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. 
,
@lcs-25
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. 

stem4x: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_solute.pdb 
ATOMS
the list of atoms (use lcs)
=
@lcs-39
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. 
,
@lcs-40
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. 
,
@lcs-41
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. 
,
@lcs-42
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information. 
,
@lcs-47
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 47. Click here for more information. 
,
@lcs-48
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 48. Click here for more information. 
,
@lcs-49
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 49. Click here for more information. 
,
@lcs-50
an 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

INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=cg_map.dat

SAXS
Calculates SAXS intensity. More details
 ...

LABEL
a label for the action so that its output can be referenced in the input to other actions
=saxs

ATOMS
The 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

QVALUE1
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.001

QVALUE2
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.025

QVALUE3
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.05

QVALUE4
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.075

QVALUE5
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.1

QVALUE6
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.2

QVALUE7
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.25

QVALUE8
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.35
... SAXS

SAXS
Calculates SAXS intensity. More details
 ...

LABEL
a label for the action so that its output can be referenced in the input to other actions
=saxs_bias


ATOMS
The 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

QVALUE1
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.1

QVALUE2
Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, 
=0.2
... SAXS

ratio: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
FUNC
the function you wish to evaluate
=(a*0.01)/(b*0.04 
ARG
the input for this action is the scalar output from one or more other actions
=saxs_bias.q-0,saxs_bias.q-1 
VAR
the names to give each of the arguments in the function
=a,b 
PERIODIC
if 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
uwall1: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=stem1x 
AT
the positions of the wall
=0.7 
KAPPA
the 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
uwall2: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=stem2x 
AT
the positions of the wall
=0.7 
KAPPA
the 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
uwall3: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=stem3x 
AT
the positions of the wall
=0.7 
KAPPA
the 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
uwall4: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=stem4x 
AT
the positions of the wall
=0.7 
KAPPA
the 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

lwall:  
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Rg 
AT
the positions of the wall
=1.60 
KAPPA
the 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
uwall:  
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Rg 
AT
the positions of the wall
=2.5  
KAPPA
the 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

uwall_ratio:  
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ratio 
AT
the positions of the wall
=2.7  
KAPPA
the 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
meta: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ratio,diff 
SIGMA
the widths of the Gaussian hills
=0.035,0.05 
HEIGHT
the heights of the Gaussian hills
=2.09 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
PACE
the frequency for hill addition
=400 
GRID_MIN
the lower bounds for the grid
=0,0 
GRID_MAX
the upper bounds for the grid
=8,14 
STRIDE
the frequency with which the forces due to the bias should be calculated
=2

# print stuff

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(saxs\.q-.*),ratio 
FILE
the 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

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Rg,ratio,diff,full,(stem.),(.*x),meta.bias,(uwall.\.bias),lwall.bias,uwall.bias,uwall_ratio.bias 
FILE
the 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