PLUMED-NEST

Project ID: plumID:20.034
Source: plumed_SL1.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

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
=SL1_ext_gmx.pdb 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=rna

# ermsd from helix 1. the large cutoff is used for pulling, the default cutoff for monitoring 
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
=SL1_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-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. 
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
=SL1_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-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. 
 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=12

# ermsd from helix 2
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
=SL1_target_p2.pdb 
ATOMS
the list of atoms (use lcs)
=
@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-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. 
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
=SL1_target_p2.pdb 
ATOMS
the list of atoms (use lcs)
=
@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-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. 
 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=12

# calculate distances between ring centers
The ERMSD action with label ermsd1_p2 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. 

c24: 
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-24
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 24. Click here for more information. 
c25: 
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-25
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 25. 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. 
c29: 
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-29
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 29. 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. 
c9: 
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-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. 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. 
c12: 
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-12
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 

c17: 
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-17
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 17. 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. 
c21: 
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-21
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 21. 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,c29
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,c28
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,c27
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,c26
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,c25
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,c24

The DISTANCE action with label dp1_6 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
=c8,c21
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
=c9,c20
The DISTANCE action with label dp2_2 calculates a scalar quantitydp2_3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c10,c19
The DISTANCE action with label dp2_3 calculates a scalar quantitydp2_4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c11,c18
The DISTANCE action with label dp2_4 calculates a scalar quantitydp2_5: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c12,c17

# ABMD: spring constant is set to 2 kj/mol, and stops acting when reaches 1
The DISTANCE action with label dp2_5 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,ermsd1_p2
KAPPA
The array of force constants
=2,2
TO
The array of target values
=1,1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=qq 
... ABMD

The ABMD action with label qq calculates the following quantities:
 Quantity   
 Description  
qq.bias
the instantaneous value of the bias potential
qq.force2
the instantaneous value of the squared force due to this bias potential
qq._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
=DIST_2 
ARG
the input for this action is the scalar output from one or more other actions
=ermsd0_p1,ermsd0_p2,ermsd1_p1,ermsd1_p2,qq.bias,dp1_1,dp1_2,dp1_3,dp1_4,dp1_5,dp1_6,dp2_1,dp2_2,dp2_3,dp2_4,dp2_5 
STRIDE
 the frequency with which the quantities of interest should be output
=5000