PLUMED-NEST

Project ID: plumID:20.034
Source: plumed_SL5A.dat
Originally used with PLUMED version: 2.5.3
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

RESTARTActivate restart. More details
The RESTART action with label  calculates somethingMOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=SL5a_ext_gmx.pdb MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=rna


ermsd0_p1The ERMSD action with label ermsd0_p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
ermsd0_p1
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL5a_H1_template.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-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. 
ermsd0_p1: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL5a_H1_template.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-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.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
ermsd1_p1The ERMSD action with label ermsd1_p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
ermsd1_p1
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL5a_H1_template.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-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.  CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=12

ermsd0_p2The ERMSD action with label ermsd0_p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
ermsd0_p2
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL5a_H2_template.pdb ATOMSthe list of atoms (use lcs)=@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@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-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. 
ermsd0_p2: ERMSDCalculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL5a_H2_template.pdb ATOMSthe list of atoms (use lcs)=@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@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-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.   CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=2.4
ermsd1_p2The ERMSD action with label ermsd1_p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
ermsd1_p2
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: ERMSDCalculate eRMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=SL5a_H2_template.pdb ATOMSthe list of atoms (use lcs)=@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. ,@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. ,@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. ,@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-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.  CUTOFF only pairs of atoms closer than CUTOFF are considered in the calculation=12


# HELIX1 
c1The CENTER_FAST action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-1an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
c2The CENTER_FAST action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-2an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
c3The CENTER_FAST action with label c3 calculates the following quantities:
 Quantity   
 Type   
 Description  
c3
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-3an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
c4The CENTER_FAST action with label c4 calculates the following quantities:
 Quantity   
 Type   
 Description  
c4
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-4an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
c5The CENTER_FAST action with label c5 calculates the following quantities:
 Quantity   
 Type   
 Description  
c5
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-5an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
c6The CENTER_FAST action with label c6 calculates the following quantities:
 Quantity   
 Type   
 Description  
c6
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-6an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
c7The CENTER_FAST action with label c7 calculates the following quantities:
 Quantity   
 Type   
 Description  
c7
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-7an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 

c27The CENTER_FAST action with label c27 calculates the following quantities:
 Quantity   
 Type   
 Description  
c27
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-27an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 27. Click here for more information. 
c28The CENTER_FAST action with label c28 calculates the following quantities:
 Quantity   
 Type   
 Description  
c28
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-28an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 28. Click here for more information. 
c29The CENTER_FAST action with label c29 calculates the following quantities:
 Quantity   
 Type   
 Description  
c29
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-29an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. Click here for more information. 
c30The CENTER_FAST action with label c30 calculates the following quantities:
 Quantity   
 Type   
 Description  
c30
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-30an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 30. Click here for more information. 
c31The CENTER_FAST action with label c31 calculates the following quantities:
 Quantity   
 Type   
 Description  
c31
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-31an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 31. Click here for more information. 
c32The CENTER_FAST action with label c32 calculates the following quantities:
 Quantity   
 Type   
 Description  
c32
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-32an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 32. Click here for more information. 
c33The CENTER_FAST action with label c33 calculates the following quantities:
 Quantity   
 Type   
 Description  
c33
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-33an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 33. Click here for more information. 

# HELIX2
c9The CENTER_FAST action with label c9 calculates the following quantities:
 Quantity   
 Type   
 Description  
c9
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-9an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
c10The CENTER_FAST action with label c10 calculates the following quantities:
 Quantity   
 Type   
 Description  
c10
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-10an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. 
c11The CENTER_FAST action with label c11 calculates the following quantities:
 Quantity   
 Type   
 Description  
c11
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-11an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 
c12The CENTER_FAST action with label c12 calculates the following quantities:
 Quantity   
 Type   
 Description  
c12
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-12an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 
c13The CENTER_FAST action with label c13 calculates the following quantities:
 Quantity   
 Type   
 Description  
c13
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-13an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 

c20The CENTER_FAST action with label c20 calculates the following quantities:
 Quantity   
 Type   
 Description  
c20
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-20an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 20. Click here for more information. 
c21The CENTER_FAST action with label c21 calculates the following quantities:
 Quantity   
 Type   
 Description  
c21
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-21an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. Click here for more information. 
c22The CENTER_FAST action with label c22 calculates the following quantities:
 Quantity   
 Type   
 Description  
c22
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-22an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 22. Click here for more information. 
c23The CENTER_FAST action with label c23 calculates the following quantities:
 Quantity   
 Type   
 Description  
c23
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-23an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 23. Click here for more information. 
c24The CENTER_FAST action with label c24 calculates the following quantities:
 Quantity   
 Type   
 Description  
c24
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-24an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. 


dp1_1The DISTANCE action with label dp1_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp1_1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c33
dp1_2The DISTANCE action with label dp1_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp1_2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c2,c32
dp1_3The DISTANCE action with label dp1_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp1_3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c3,c31
dp1_4The DISTANCE action with label dp1_4 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp1_4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c4,c30
dp1_5The DISTANCE action with label dp1_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp1_5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c5,c29
dp1_6The DISTANCE action with label dp1_6 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp1_6
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c6,c28
dp1_7The DISTANCE action with label dp1_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp1_7
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c7,c27

dp2_1The DISTANCE action with label dp2_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp2_1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c9,c24
dp2_2The DISTANCE action with label dp2_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp2_2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c10,c23
dp2_3The DISTANCE action with label dp2_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp2_3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c11,c22
dp2_4The DISTANCE action with label dp2_4 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp2_4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c12,c21
dp2_5The DISTANCE action with label dp2_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
dp2_5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c13,c20


# other 
c8The CENTER_FAST action with label c8 calculates the following quantities:
 Quantity   
 Type   
 Description  
c8
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-8an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
c14The CENTER_FAST action with label c14 calculates the following quantities:
 Quantity   
 Type   
 Description  
c14
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-14an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
c15The CENTER_FAST action with label c15 calculates the following quantities:
 Quantity   
 Type   
 Description  
c15
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-15an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 15. Click here for more information. 
c18The CENTER_FAST action with label c18 calculates the following quantities:
 Quantity   
 Type   
 Description  
c18
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-18an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 18. Click here for more information. 
c19The CENTER_FAST action with label c19 calculates the following quantities:
 Quantity   
 Type   
 Description  
c19
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-19an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 19. Click here for more information. 
c25The CENTER_FAST action with label c25 calculates the following quantities:
 Quantity   
 Type   
 Description  
c25
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-25an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. Click here for more information. 
c26The CENTER_FAST action with label c26 calculates the following quantities:
 Quantity   
 Type   
 Description  
c26
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=@lcs-26an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 26. Click here for more information. 

D8_25The DISTANCE action with label D8_25 calculates the following quantities:
 Quantity   
 Type   
 Description  
D8_25
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c8,c25
D8_26The DISTANCE action with label D8_26 calculates the following quantities:
 Quantity   
 Type   
 Description  
D8_26
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c8,c26
D14_19The DISTANCE action with label D14_19 calculates the following quantities:
 Quantity   
 Type   
 Description  
D14_19
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c14,c19
D15_18The DISTANCE action with label D15_18 calculates the following quantities:
 Quantity   
 Type   
 Description  
D15_18
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c15,c18

chiThe TORSION action with label chi calculates the following quantities:
 Quantity   
 Type   
 Description  
chi
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@chi-18the four atoms that are required to alcullate the chi dihedral for residue 18. Click here for more information. 

ABMDAdds a ratchet-and-pawl like restraint on one or more variables. More details ... 
ARGthe labels of the scalars on which the bias will act=ermsd1_p1,ermsd1_p2
KAPPAThe array of force constants=1,1
TOThe array of target values=1,1 
LABELa label for the action so that its output can be referenced in the input to other actions=qqThe ABMD action with label qq calculates the following quantities:
 Quantity   
 Type   
 Description  
qq.bias
scalar
the instantaneous value of the bias potential
qq.ermsd1_p1_min
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named ermsd1_p1
qq.ermsd1_p2_min
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named ermsd1_p2
qq.force2
scalar
the instantaneous value of the squared force due to this bias potential 
... ABMD

PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=ERMSD_YYY ARGthe labels of the values that you would like to print to the file=ermsd0_p1,ermsd0_p2,ermsd1_p1,ermsd1_p2,qq.bias STRIDE the frequency with which the quantities of interest should be output=5000
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=DIST_YYY ARGthe labels of the values that you would like to print to the file=dp1_1,dp1_2,dp1_3,dp1_4,dp1_5,dp1_6,dp1_7,dp2_1,dp2_2,dp2_3,dp2_4,dp2_5,D8_25,D8_26,D14_19,D15_18,chi STRIDE the frequency with which the quantities of interest should be output=5000