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

RESTART
Activate restart. 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
=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_p1: 
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
=SL4_target_p1.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-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. 
The ERMSD action with label ermsd0_p1 calculates a scalar quantityermsd1_p1: 
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
=SL4_target_p1.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-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. 
 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=12

The ERMSD action with label ermsd1_p1 calculates a scalar quantityermsd0_p2: 
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
=SL4_target_p2.pdb 
ATOMS
the list of atoms (use lcs)
=
@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-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. 
The ERMSD action with label ermsd0_p2 calculates a scalar quantityermsd1_p2: 
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
=SL4_target_p2.pdb 
ATOMS
the list of atoms (use lcs)
=
@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-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. 
 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=12

The ERMSD action with label ermsd1_p2 calculates a scalar quantityermsd0_p3: 
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
=SL4_target_p3.pdb 
ATOMS
the list of atoms (use lcs)
=
@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-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. 
The ERMSD action with label ermsd0_p3 calculates a scalar quantityermsd1_p3: 
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
=SL4_target_p3.pdb 
ATOMS
the list of atoms (use lcs)
=
@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-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. 
 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=12

The ERMSD action with label ermsd1_p3 calculates a scalar quantityermsd0_p4: 
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
=SL4_target_p4.pdb 
ATOMS
the list of atoms (use lcs)
=
@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-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. 
The ERMSD action with label ermsd0_p4 calculates a scalar quantityermsd1_p4: 
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
=SL4_target_p4.pdb 
ATOMS
the list of atoms (use lcs)
=
@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-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. 
 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=12

# print the distance between different bases 
The ERMSD action with label ermsd1_p4 calculates a scalar quantityc1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
c2: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
c3: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
c4: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
c5: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
c6: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
c7: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
c8: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 

c10: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-10
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. 
c11: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-11
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 

c13: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-13
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
c14: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-14
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
c15: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-15
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. 
c16: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-16
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 16. Click here for more information. 

c18: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-18
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. 
c19: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-19
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. 
c20: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-20
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. 

c26: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-26
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. 
c27: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-27
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. 
c28: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-28
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. 

c30: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-30
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. 
c31: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-31
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. 
c32: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-32
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. 
c33: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-33
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information. 

c34: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-34
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 34. Click here for more information. 
c35: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-35
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 35. Click here for more information. 


c37: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-37
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 37. Click here for more information. 
c38: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-38
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 38. Click here for more information. 
c39: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-39
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 39. Click here for more information. 
c40: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-40
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 40. Click here for more information. 
c41: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-41
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 41. Click here for more information. 
c42: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-42
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 42. Click here for more information. 
c43: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-43
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 43. Click here for more information. 
c44: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@lcs-44
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 44. Click here for more information. 


dp1_1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c1,c44
The DISTANCE action with label dp1_1 calculates a scalar quantitydp1_2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c2,c43
The DISTANCE action with label dp1_2 calculates a scalar quantitydp1_3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c3,c42
The DISTANCE action with label dp1_3 calculates a scalar quantitydp1_4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c4,c41
The DISTANCE action with label dp1_4 calculates a scalar quantitydp1_5: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c5,c40
The DISTANCE action with label dp1_5 calculates a scalar quantitydp1_6: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c6,c39
The DISTANCE action with label dp1_6 calculates a scalar quantitydp1_7: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c7,c38
The DISTANCE action with label dp1_7 calculates a scalar quantitydp1_8: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c8,c37

The DISTANCE action with label dp1_8 calculates a scalar quantitydp2_1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c10,c35
The DISTANCE action with label dp2_1 calculates a scalar quantitydp2_2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c11,c34

The DISTANCE action with label dp2_2 calculates a scalar quantitydp3_1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c13,c33
The DISTANCE action with label dp3_1 calculates a scalar quantitydp3_2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c14,c32
The DISTANCE action with label dp3_2 calculates a scalar quantitydp3_3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c15,c31
The DISTANCE action with label dp3_3 calculates a scalar quantitydp3_4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c16,c30

The DISTANCE action with label dp3_4 calculates a scalar quantitydp4_1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c18,c28
The DISTANCE action with label dp4_1 calculates a scalar quantitydp4_2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c19,c27
The DISTANCE action with label dp4_2 calculates a scalar quantitydp4_3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the 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
The DISTANCE action with label dp4_3 calculates a scalar quantity
ABMD
Adds a ratchet-and-pawl like restraint on one or more variables. More details
 ... 
ARG
the input for this action is the scalar output from one or more other actions
=ermsd1_p1
KAPPA
The array of force constants
=4
TO
The array of target values
=1
LABEL
a label for the action so that its output can be referenced in the input to other actions
=qq1 
... ABMD

The ABMD action with label qq1 calculates the following quantities:
 Quantity   
 Description  
qq1.bias
the instantaneous value of the bias potential
qq1.force2
the instantaneous value of the squared force due to this bias potential
qq1._min
one or multiple instances of this quantity can be referenced elsewhere in the input file
ABMD
Adds a ratchet-and-pawl like restraint on one or more variables. More details
 ... 
ARG
the input for this action is the scalar output from one or more other actions
=ermsd1_p2
KAPPA
The array of force constants
=4
TO
The array of target values
=1
LABEL
a label for the action so that its output can be referenced in the input to other actions
=qq2
... ABMD

The ABMD action with label qq2 calculates the following quantities:
 Quantity   
 Description  
qq2.bias
the instantaneous value of the bias potential
qq2.force2
the instantaneous value of the squared force due to this bias potential
qq2._min
one or multiple instances of this quantity can be referenced elsewhere in the input file
ABMD
Adds a ratchet-and-pawl like restraint on one or more variables. More details
 ... 
ARG
the input for this action is the scalar output from one or more other actions
=ermsd1_p3
KAPPA
The array of force constants
=4
TO
The array of target values
=1
LABEL
a label for the action so that its output can be referenced in the input to other actions
=qq3 
... ABMD

The ABMD action with label qq3 calculates the following quantities:
 Quantity   
 Description  
qq3.bias
the instantaneous value of the bias potential
qq3.force2
the instantaneous value of the squared force due to this bias potential
qq3._min
one or multiple instances of this quantity can be referenced elsewhere in the input file
ABMD
Adds a ratchet-and-pawl like restraint on one or more variables. More details
 ... 
ARG
the input for this action is the scalar output from one or more other actions
=ermsd1_p4
KAPPA
The array of force constants
=4
TO
The array of target values
=1
LABEL
a label for the action so that its output can be referenced in the input to other actions
=qq4 
... ABMD

The ABMD action with label qq4 calculates the following quantities:
 Quantity   
 Description  
qq4.bias
the instantaneous value of the bias potential
qq4.force2
the instantaneous value of the squared force due to this bias potential
qq4._min
one or multiple instances of this quantity can be referenced elsewhere in the input file
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=Q_YYY 
ARG
the input for this action is the scalar output from one or more other actions
=qq1.bias,qq2.bias,qq3.bias,qq4.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=5000
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=ERMSD_YYY 
ARG
the input for this action is the scalar output from one or more other actions
=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
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=DIST_YYY 
ARG
the input for this action is the scalar output from one or more other actions
=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