Project ID: plumID:23.008
Source: plumed_analysis.dat
Originally used with PLUMED version: 2.5.0
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

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
=hst5.pdb
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
=1-417
phi2:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi3:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi4:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi5:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-5
the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi6:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-6
the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi7:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-7
the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi8:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-8
the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi9:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-9
the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi10:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-10
the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi11:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-11
the four atoms that are required to calculate the phi dihedral for residue 11. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi12:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-12
the four atoms that are required to calculate the phi dihedral for residue 12. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi13:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-13
the four atoms that are required to calculate the phi dihedral for residue 13. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi14:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-14
the four atoms that are required to calculate the phi dihedral for residue 14. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi15:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-15
the four atoms that are required to calculate the phi dihedral for residue 15. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi16:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-16
the four atoms that are required to calculate the phi dihedral for residue 16. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi17:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-17
the four atoms that are required to calculate the phi dihedral for residue 17. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi18:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-18
the four atoms that are required to calculate the phi dihedral for residue 18. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi19:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-19
the four atoms that are required to calculate the phi dihedral for residue 19. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi20:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-20
the four atoms that are required to calculate the phi dihedral for residue 20. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi21:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-21
the four atoms that are required to calculate the phi dihedral for residue 21. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi22:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-22
the four atoms that are required to calculate the phi dihedral for residue 22. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi23:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-23
the four atoms that are required to calculate the phi dihedral for residue 23. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
phi24:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@phi-24
the four atoms that are required to calculate the phi dihedral for residue 24. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances

psi1:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi2:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi3:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi4:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi5:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi6:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi7:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi8:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi9:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi10:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi11:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi12:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi13:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi14:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi15:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi16:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi17:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi18:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi19:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi20:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-20
the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi21:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-21
the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi22:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-22
the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
psi23:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=
@psi-23
the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances

ca:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
NDX_FILE
the name of index file (gromacs syntax)
=hst5.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=C-alpha rg:
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1-417
NOPBC
ignore the periodic boundary conditions when calculating distances

PBMETAD
Used to performed Parallel Bias metadynamics. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pbmetad
WALKERS_MPI
Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
ARG
the input for this action is the scalar output from one or more other actions
=phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,phi10,phi11,phi12,phi13,phi14,phi15,phi16,phi17,phi18,phi19,phi20,phi21,phi22,phi23,phi24,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,psi9,psi10,psi11,psi12,psi13,psi14,psi15,psi16,psi17,psi18,psi19,psi20,psi21,psi22,psi23,rg
PACE
the frequency for hill addition, one for all biases
=90000000
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=24
HEIGHT
the height of the Gaussian hills, one for all biases
=0.3
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
SIGMA
the widths of the Gaussian hills
=1000
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.001
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.4
GRID_MIN
the lower bounds for the grid
=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0.4
GRID_MAX
the upper bounds for the grid
=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,2.8
INTERVAL_MIN
one dimensional lower limits, outside the limits the system will not feel the biasing force
=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0.60
INTERVAL_MAX
one dimensional upper limits, outside the limits the system will not feel the biasing force
=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,2.50 #GRID_RFILES=GRID.phi2,GRID.phi3,GRID.phi4,GRID.phi5,GRID.phi6,GRID.phi7,GRID.phi8,GRID.phi9,GRID.phi10,GRID.phi11,GRID.phi12,GRID.phi13,GRID.phi14,GRID.phi15,GRID.phi16,GRID.phi17,GRID.phi18,GRID.phi19,GRID.phi20,GRID.phi21,GRID.phi22,GRID.phi23,GRID.phi24,GRID.psi1,GRID.psi2,GRID.psi3,GRID.psi4,GRID.psi5,GRID.psi6,GRID.psi7,GRID.psi8,GRID.psi9,GRID.psi10,GRID.psi11,GRID.psi12,GRID.psi13,GRID.psi14,GRID.psi15,GRID.psi16,GRID.psi17,GRID.psi18,GRID.psi19,GRID.psi20,GRID.psi21,GRID.psi22,GRID.psi23,GRID.rg
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310 ... PBMETAD
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=1
FILE
the name of the file on which to output these quantities
=CV_PHI
ARG
the input for this action is the scalar output from one or more other actions
=phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,phi10,phi11,phi12,phi13,phi14,phi15,phi16,phi17,phi18,phi19,phi20,phi21,phi22,phi23,phi24
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=1
FILE
the name of the file on which to output these quantities
=CV_PSI
ARG
the input for this action is the scalar output from one or more other actions
=psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,psi9,psi10,psi11,psi12,psi13,psi14,psi15,psi16,psi17,psi18,psi19,psi20,psi21,psi22,psi23
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=1
FILE
the name of the file on which to output these quantities
=RG_BIAS
ARG
the input for this action is the scalar output from one or more other actions
=rg,pbmetad.bias