PLUMED-NEST

Project ID: plumID:19.070
Source: plumed_nest_uucg/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

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
=2koc_gmx.pdb
The MOLINFO action with label  calculates something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-447
e3The ERMSD action with label e3 calculates the following quantities:
 Quantity   
 Type   
 Description  
e3
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: 
ERMSD
Calculate eRMSD with respect to a reference structure. This action has hidden defaults. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
,
@lcs-10
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. 
,
@lcs-11
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 
,
@lcs-12
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 
,
@lcs-13
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
,
@lcs-14
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
  
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=2koc_gmx.pdb
e3: 
ERMSD
Calculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
,
@lcs-10
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. 
,
@lcs-11
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 
,
@lcs-12
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 
,
@lcs-13
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
,
@lcs-14
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
  
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=2koc_gmx.pdb  
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=2.4
ee3The ERMSD action with label ee3 calculates the following quantities:
 Quantity   
 Type   
 Description  
ee3
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information. 
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information. 
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
,
@lcs-10
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 10. Click here for more information. 
,
@lcs-11
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 11. Click here for more information. 
,
@lcs-12
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 12. Click here for more information. 
,
@lcs-13
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 13. Click here for more information. 
,
@lcs-14
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 14. Click here for more information. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=2koc_gmx.pdb 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=3.2
estemThe ERMSD action with label estem calculates the following quantities:
 Quantity   
 Type   
 Description  
estem
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: 
ERMSD
Calculate eRMSD with respect to a reference structure. This action has hidden defaults. More details
 
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-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. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=2koc_gmx.pdb
estem: 
ERMSD
Calculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details
 
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-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. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=2koc_gmx.pdb  
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=2.4
eloopThe ERMSD action with label eloop calculates the following quantities:
 Quantity   
 Type   
 Description  
eloop
scalar
the eRMSD between the instantaneous structure and the reference structure that was input: 
ERMSD
Calculate eRMSD with respect to a reference structure. This action has hidden defaults. More details
 
ATOMS
the list of atoms (use lcs)
=
@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. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=2koc_gmx.pdb
eloop: 
ERMSD
Calculate eRMSD with respect to a reference structure. This action uses the defaults shown here. More details
 
ATOMS
the list of atoms (use lcs)
=
@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. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=2koc_gmx.pdb  
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=2.4

r3The RMSD action with label r3 calculates the following quantities:
 Quantity   
 Type   
 Description  
r3
scalar
the RMSD between the instantaneous structure and the reference structure that was input: 
RMSD
Calculate the RMSD with respect to a reference structure. This action has hidden defaults. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=2koc_gmx.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
r3: 
RMSD
Calculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=2koc_gmx.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL  
NUMBER
 if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here
=0
zeta8The TORSION action with label zeta8 calculates the following quantities:
 Quantity   
 Type   
 Description  
zeta8
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@zeta-8
the four atoms that are required to calculate the zeta backbone dihedral for residue 8. Click here for more information. 
delta8The TORSION action with label delta8 calculates the following quantities:
 Quantity   
 Type   
 Description  
delta8
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@delta-8
the four atoms that are required to calculate the delta backbone dihedral for residue 8. Click here for more information. 
ddThe DISTANCE action with label dd calculates the following quantities:
 Quantity   
 Type   
 Description  
dd
scalar
the DISTANCE between this pair of atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=184,273

metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ee3 
PACE
the frequency for hill addition
=500 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=70 
SIGMA
the widths of the Gaussian hills
=0.5 
FILE
 a file in which the list of added hills is stored
=HILLS 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=278 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
GRID_MIN
the lower bounds for the grid
=0 
GRID_MAX
the upper bounds for the grid
=6.0 
GRID_BIN
the number of bins for the grid
=300

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=e3,ee3,estem,eloop,r3,zeta8,delta8,dd  
FILE
the name of the file on which to output these quantities
=colvar 
STRIDE
 the frequency with which the quantities of interest should be output
=1000