Project ID: plumID:22.035
Source: allD_helix.dat
Originally used with PLUMED version: 2.6.1
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
# Define CVs. Phi, psi
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
=allD_helix_H.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
=1-330
# Dihedral angles 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

PBMETAD
Used to performed Parallel Bias metadynamics. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=psi1,psi2,phi2,psi3,phi3,psi4,phi4,psi5,phi5,psi6,phi6,psi7,phi7,psi8,phi8,psi9,phi9,psi10,phi10,psi11,phi11,psi12,phi12,psi13,phi13,psi14,phi14,psi15,phi15,psi16,phi16,psi17,phi17,psi18,phi18,psi19,phi19,psi20,phi20,psi21,phi21,phi22
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
SIGMA
the widths of the Gaussian hills
=1000
PACE
the frequency for hill addition, one for all biases
=200
HEIGHT
the height of the Gaussian hills, one for all biases
=0.3
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=32
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pb
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6
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
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
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
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
GRID_WSTRIDE
frequency for dumping the grid
=500000000 ... PBMETAD