Project ID: plumID:20.034
Source: plumed_SL2.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
tested onv2.9
tested onmaster
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
=SL2_ref.pdb
MOLTYPE
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=rna
# in this case we can monitor the distance from the reference NMR structure ermsd0:
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
=SL2_NMR_template.pdb
ATOMS
the list of atoms (use lcs)
=
@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.

ermsd_target:
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
=SL2_match.pdb
ATOMS
the list of atoms (use lcs)
=
@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-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.
CUTOFF
only pairs of atoms closer than CUTOFF are considered in the calculation
=12 ermsd_target0:
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
=SL2_match.pdb
ATOMS
the list of atoms (use lcs)
=
@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-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.

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.

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.
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.
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.

d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=c2,c16 d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=c3,c15 d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=c4,c14 d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=c5,c13 d5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=c6,c12 d6:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=c7,c10
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
=ermsd_target
KAPPA
The array of force constants
=2.0
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
=qq0 ... ABMD
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
=ermsd0,ermsd_target,ermsd_target0,d1,d2,d3,d4,d5,d6,qq0.bias
STRIDE
the frequency with which the quantities of interest should be output
=5000