PLUMED-NEST

Project ID: plumID:22.028
Source: plumed_FM5.dat
Originally used with PLUMED version: 2.7
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

######### PLUMED file for performing RECT simulations on N-glycans #########
#
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
=reference_FM5.pdb
#
# Define torsion angles for FM5
#
phi1_2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O5-2
the O5 atom in residue 2. Click here for more information. 
,
@C1-2
the C1 atom in residue 2. Click here for more information. 
,
@O4-1
the O4 atom in residue 1. Click here for more information. 
,
@C4-1
the C4 atom in residue 1. Click here for more information. 
The TORSION action with label phi1_2 calculates a scalar quantitypsi1_2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@C1-2
the C1 atom in residue 2. Click here for more information. 
,
@O4-1
the O4 atom in residue 1. Click here for more information. 
,
@C4-1
the C4 atom in residue 1. Click here for more information. 
,
@C3-1
the C3 atom in residue 1. Click here for more information. 
#
The TORSION action with label psi1_2 calculates a scalar quantityphi2_3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O5-3
the O5 atom in residue 3. Click here for more information. 
,
@C1-3
the C1 atom in residue 3. Click here for more information. 
,
@O4-2
the O4 atom in residue 2. Click here for more information. 
,
@C4-2
the C4 atom in residue 2. Click here for more information. 
The TORSION action with label phi2_3 calculates a scalar quantitypsi2_3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@C1-3
the C1 atom in residue 3. Click here for more information. 
,
@O4-2
the O4 atom in residue 2. Click here for more information. 
,
@C4-2
the C4 atom in residue 2. Click here for more information. 
,
@C3-2
the C3 atom in residue 2. Click here for more information. 
#
The TORSION action with label psi2_3 calculates a scalar quantityphi3_4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O5-4
the O5 atom in residue 4. Click here for more information. 
,
@C1-4
the C1 atom in residue 4. Click here for more information. 
,
@O3-3
the O3 atom in residue 3. Click here for more information. 
,
@C3-3
the C3 atom in residue 3. Click here for more information. 
The TORSION action with label phi3_4 calculates a scalar quantitypsi3_4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@C1-4
the C1 atom in residue 4. Click here for more information. 
,
@O3-3
the O3 atom in residue 3. Click here for more information. 
,
@C3-3
the C3 atom in residue 3. Click here for more information. 
,
@C2-3
the C2 atom in residue 3. Click here for more information. 
#
The TORSION action with label psi3_4 calculates a scalar quantityphi3_5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O5-5
the O5 atom in residue 5. Click here for more information. 
,
@C1-5
the C1 atom in residue 5. Click here for more information. 
,
@O6-3
the O6 atom in residue 3. Click here for more information. 
,
@C6-3
the C6 atom in residue 3. Click here for more information. 
The TORSION action with label phi3_5 calculates a scalar quantitypsi3_5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@C1-5
the C1 atom in residue 5. Click here for more information. 
,
@O6-3
the O6 atom in residue 3. Click here for more information. 
,
@C6-3
the C6 atom in residue 3. Click here for more information. 
,
@C5-3
the C5 atom in residue 3. Click here for more information. 
The TORSION action with label psi3_5 calculates a scalar quantityomega3_5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O6-3
the O6 atom in residue 3. Click here for more information. 
,
@C6-3
the C6 atom in residue 3. Click here for more information. 
,
@C5-3
the C5 atom in residue 3. Click here for more information. 
,
@O5-3
the O5 atom in residue 3. Click here for more information. 
#
The TORSION action with label omega3_5 calculates a scalar quantityphi5_7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O5-7
the O5 atom in residue 7. Click here for more information. 
,
@C1-7
the C1 atom in residue 7. Click here for more information. 
,
@O6-5
the O6 atom in residue 5. Click here for more information. 
,
@C6-5
the C6 atom in residue 5. Click here for more information. 
The TORSION action with label phi5_7 calculates a scalar quantitypsi5_7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@C1-7
the C1 atom in residue 7. Click here for more information. 
,
@O6-5
the O6 atom in residue 5. Click here for more information. 
,
@C6-5
the C6 atom in residue 5. Click here for more information. 
,
@C5-5
the C5 atom in residue 5. Click here for more information. 
The TORSION action with label psi5_7 calculates a scalar quantityomega5_7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O6-5
the O6 atom in residue 5. Click here for more information. 
,
@C6-5
the C6 atom in residue 5. Click here for more information. 
,
@C5-5
the C5 atom in residue 5. Click here for more information. 
,
@O5-5
the O5 atom in residue 5. Click here for more information. 
#
The TORSION action with label omega5_7 calculates a scalar quantityphi5_6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O5-6
the O5 atom in residue 6. Click here for more information. 
,
@C1-6
the C1 atom in residue 6. Click here for more information. 
,
@O3-5
the O3 atom in residue 5. Click here for more information. 
,
@C3-5
the C3 atom in residue 5. Click here for more information. 
The TORSION action with label phi5_6 calculates a scalar quantitypsi5_6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@C1-6
the C1 atom in residue 6. Click here for more information. 
,
@O3-5
the O3 atom in residue 5. Click here for more information. 
,
@C3-5
the C3 atom in residue 5. Click here for more information. 
,
@C2-5
the C2 atom in residue 5. Click here for more information. 
#
The TORSION action with label psi5_6 calculates a scalar quantityphi1_8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O5-8
the O5 atom in residue 8. Click here for more information. 
,
@C1-8
the C1 atom in residue 8. Click here for more information. 
,
@O6-1
the O6 atom in residue 1. Click here for more information. 
,
@C6-1
the C6 atom in residue 1. Click here for more information. 
The TORSION action with label phi1_8 calculates a scalar quantitypsi1_8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@C1-8
the C1 atom in residue 8. Click here for more information. 
,
@O6-1
the O6 atom in residue 1. Click here for more information. 
,
@C6-1
the C6 atom in residue 1. Click here for more information. 
,
@C5-1
the C5 atom in residue 1. Click here for more information. 
The TORSION action with label psi1_8 calculates a scalar quantityomega1_8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@O6-1
the O6 atom in residue 1. Click here for more information. 
,
@C6-1
the C6 atom in residue 1. Click here for more information. 
,
@C5-1
the C5 atom in residue 1. Click here for more information. 
,
@O5-1
the O5 atom in residue 1. Click here for more information. 
#
# Define puckering for each monosaccharide only to print it to file
#
The TORSION action with label omega1_8 calculates a scalar quantitypuck1: 
PUCKERING
 Calculate sugar pseudorotation coordinates. More details
 
ATOMS
the five or six atoms of the sugar ring in the proper order
=
@O5-1
the O5 atom in residue 1. Click here for more information. 
,
@C1-1
the C1 atom in residue 1. Click here for more information. 
,
@C2-1
the C2 atom in residue 1. Click here for more information. 
,
@C3-1
the C3 atom in residue 1. Click here for more information. 
,
@C4-1
the C4 atom in residue 1. Click here for more information. 
,
@C5-1
the C5 atom in residue 1. Click here for more information. 
The PUCKERING action with label puck1 calculates the following quantities:
 Quantity   
 Description  
puck1.phs
Pseudorotation phase (5 membered rings)
puck1.amp
Pseudorotation amplitude (5 membered rings)
puck1.Zx
Pseudorotation x Cartesian component (5 membered rings)
puck1.Zy
Pseudorotation y Cartesian component (5 membered rings)
puck1.phi
Pseudorotation phase (6 membered rings)
puck1.theta
Theta angle (6 membered rings)
puck1.amplitude
Pseudorotation amplitude (6 membered rings)
puck1.qx
Cartesian component x (6 membered rings)
puck1.qy
Cartesian component y (6 membered rings)
puck1.qz
Cartesian component z (6 membered rings)puck2: 
PUCKERING
 Calculate sugar pseudorotation coordinates. More details
 
ATOMS
the five or six atoms of the sugar ring in the proper order
=
@O5-2
the O5 atom in residue 2. Click here for more information. 
,
@C1-2
the C1 atom in residue 2. Click here for more information. 
,
@C2-2
the C2 atom in residue 2. Click here for more information. 
,
@C3-2
the C3 atom in residue 2. Click here for more information. 
,
@C4-2
the C4 atom in residue 2. Click here for more information. 
,
@C5-2
the C5 atom in residue 2. Click here for more information. 
The PUCKERING action with label puck2 calculates the following quantities:
 Quantity   
 Description  
puck2.phs
Pseudorotation phase (5 membered rings)
puck2.amp
Pseudorotation amplitude (5 membered rings)
puck2.Zx
Pseudorotation x Cartesian component (5 membered rings)
puck2.Zy
Pseudorotation y Cartesian component (5 membered rings)
puck2.phi
Pseudorotation phase (6 membered rings)
puck2.theta
Theta angle (6 membered rings)
puck2.amplitude
Pseudorotation amplitude (6 membered rings)
puck2.qx
Cartesian component x (6 membered rings)
puck2.qy
Cartesian component y (6 membered rings)
puck2.qz
Cartesian component z (6 membered rings)puck3: 
PUCKERING
 Calculate sugar pseudorotation coordinates. More details
 
ATOMS
the five or six atoms of the sugar ring in the proper order
=
@O5-3
the O5 atom in residue 3. Click here for more information. 
,
@C1-3
the C1 atom in residue 3. Click here for more information. 
,
@C2-3
the C2 atom in residue 3. Click here for more information. 
,
@C3-3
the C3 atom in residue 3. Click here for more information. 
,
@C4-3
the C4 atom in residue 3. Click here for more information. 
,
@C5-3
the C5 atom in residue 3. Click here for more information. 
The PUCKERING action with label puck3 calculates the following quantities:
 Quantity   
 Description  
puck3.phs
Pseudorotation phase (5 membered rings)
puck3.amp
Pseudorotation amplitude (5 membered rings)
puck3.Zx
Pseudorotation x Cartesian component (5 membered rings)
puck3.Zy
Pseudorotation y Cartesian component (5 membered rings)
puck3.phi
Pseudorotation phase (6 membered rings)
puck3.theta
Theta angle (6 membered rings)
puck3.amplitude
Pseudorotation amplitude (6 membered rings)
puck3.qx
Cartesian component x (6 membered rings)
puck3.qy
Cartesian component y (6 membered rings)
puck3.qz
Cartesian component z (6 membered rings)puck4: 
PUCKERING
 Calculate sugar pseudorotation coordinates. More details
 
ATOMS
the five or six atoms of the sugar ring in the proper order
=
@O5-4
the O5 atom in residue 4. Click here for more information. 
,
@C1-4
the C1 atom in residue 4. Click here for more information. 
,
@C2-4
the C2 atom in residue 4. Click here for more information. 
,
@C3-4
the C3 atom in residue 4. Click here for more information. 
,
@C4-4
the C4 atom in residue 4. Click here for more information. 
,
@C5-4
the C5 atom in residue 4. Click here for more information. 
The PUCKERING action with label puck4 calculates the following quantities:
 Quantity   
 Description  
puck4.phs
Pseudorotation phase (5 membered rings)
puck4.amp
Pseudorotation amplitude (5 membered rings)
puck4.Zx
Pseudorotation x Cartesian component (5 membered rings)
puck4.Zy
Pseudorotation y Cartesian component (5 membered rings)
puck4.phi
Pseudorotation phase (6 membered rings)
puck4.theta
Theta angle (6 membered rings)
puck4.amplitude
Pseudorotation amplitude (6 membered rings)
puck4.qx
Cartesian component x (6 membered rings)
puck4.qy
Cartesian component y (6 membered rings)
puck4.qz
Cartesian component z (6 membered rings)puck5: 
PUCKERING
 Calculate sugar pseudorotation coordinates. More details
 
ATOMS
the five or six atoms of the sugar ring in the proper order
=
@O5-5
the O5 atom in residue 5. Click here for more information. 
,
@C1-5
the C1 atom in residue 5. Click here for more information. 
,
@C2-5
the C2 atom in residue 5. Click here for more information. 
,
@C3-5
the C3 atom in residue 5. Click here for more information. 
,
@C4-5
the C4 atom in residue 5. Click here for more information. 
,
@C5-5
the C5 atom in residue 5. Click here for more information. 
The PUCKERING action with label puck5 calculates the following quantities:
 Quantity   
 Description  
puck5.phs
Pseudorotation phase (5 membered rings)
puck5.amp
Pseudorotation amplitude (5 membered rings)
puck5.Zx
Pseudorotation x Cartesian component (5 membered rings)
puck5.Zy
Pseudorotation y Cartesian component (5 membered rings)
puck5.phi
Pseudorotation phase (6 membered rings)
puck5.theta
Theta angle (6 membered rings)
puck5.amplitude
Pseudorotation amplitude (6 membered rings)
puck5.qx
Cartesian component x (6 membered rings)
puck5.qy
Cartesian component y (6 membered rings)
puck5.qz
Cartesian component z (6 membered rings)puck6: 
PUCKERING
 Calculate sugar pseudorotation coordinates. More details
 
ATOMS
the five or six atoms of the sugar ring in the proper order
=
@O5-6
the O5 atom in residue 6. Click here for more information. 
,
@C1-6
the C1 atom in residue 6. Click here for more information. 
,
@C2-6
the C2 atom in residue 6. Click here for more information. 
,
@C3-6
the C3 atom in residue 6. Click here for more information. 
,
@C4-6
the C4 atom in residue 6. Click here for more information. 
,
@C5-6
the C5 atom in residue 6. Click here for more information. 
The PUCKERING action with label puck6 calculates the following quantities:
 Quantity   
 Description  
puck6.phs
Pseudorotation phase (5 membered rings)
puck6.amp
Pseudorotation amplitude (5 membered rings)
puck6.Zx
Pseudorotation x Cartesian component (5 membered rings)
puck6.Zy
Pseudorotation y Cartesian component (5 membered rings)
puck6.phi
Pseudorotation phase (6 membered rings)
puck6.theta
Theta angle (6 membered rings)
puck6.amplitude
Pseudorotation amplitude (6 membered rings)
puck6.qx
Cartesian component x (6 membered rings)
puck6.qy
Cartesian component y (6 membered rings)
puck6.qz
Cartesian component z (6 membered rings)puck7: 
PUCKERING
 Calculate sugar pseudorotation coordinates. More details
 
ATOMS
the five or six atoms of the sugar ring in the proper order
=
@O5-7
the O5 atom in residue 7. Click here for more information. 
,
@C1-7
the C1 atom in residue 7. Click here for more information. 
,
@C2-7
the C2 atom in residue 7. Click here for more information. 
,
@C3-7
the C3 atom in residue 7. Click here for more information. 
,
@C4-7
the C4 atom in residue 7. Click here for more information. 
,
@C5-7
the C5 atom in residue 7. Click here for more information. 
The PUCKERING action with label puck7 calculates the following quantities:
 Quantity   
 Description  
puck7.phs
Pseudorotation phase (5 membered rings)
puck7.amp
Pseudorotation amplitude (5 membered rings)
puck7.Zx
Pseudorotation x Cartesian component (5 membered rings)
puck7.Zy
Pseudorotation y Cartesian component (5 membered rings)
puck7.phi
Pseudorotation phase (6 membered rings)
puck7.theta
Theta angle (6 membered rings)
puck7.amplitude
Pseudorotation amplitude (6 membered rings)
puck7.qx
Cartesian component x (6 membered rings)
puck7.qy
Cartesian component y (6 membered rings)
puck7.qz
Cartesian component z (6 membered rings)puck8: 
PUCKERING
 Calculate sugar pseudorotation coordinates. More details
 
ATOMS
the five or six atoms of the sugar ring in the proper order
=
@O5-8
the O5 atom in residue 8. Click here for more information. 
,
@C1-8
the C1 atom in residue 8. Click here for more information. 
,
@C2-8
the C2 atom in residue 8. Click here for more information. 
,
@C3-8
the C3 atom in residue 8. Click here for more information. 
,
@C4-8
the C4 atom in residue 8. Click here for more information. 
,
@C5-8
the C5 atom in residue 8. Click here for more information. 
#
# Apply 1D metadynamics on each torsion angle. Different bias potentials are applied in different replicas, according to the RECT keyword. 
#
The PUCKERING action with label puck8 calculates the following quantities:
 Quantity   
 Description  
puck8.phs
Pseudorotation phase (5 membered rings)
puck8.amp
Pseudorotation amplitude (5 membered rings)
puck8.Zx
Pseudorotation x Cartesian component (5 membered rings)
puck8.Zy
Pseudorotation y Cartesian component (5 membered rings)
puck8.phi
Pseudorotation phase (6 membered rings)
puck8.theta
Theta angle (6 membered rings)
puck8.amplitude
Pseudorotation amplitude (6 membered rings)
puck8.qx
Cartesian component x (6 membered rings)
puck8.qy
Cartesian component y (6 membered rings)
puck8.qz
Cartesian component z (6 membered rings)metaD_phi1_2: 
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
=phi1_2 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_phi1_2
The METAD action with label metaD_phi1_2 calculates the following quantities:
 Quantity   
 Description  
metaD_phi1_2.bias
the instantaneous value of the bias potentialmetaD_psi1_2: 
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
=psi1_2 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_psi1_2
#
The METAD action with label metaD_psi1_2 calculates the following quantities:
 Quantity   
 Description  
metaD_psi1_2.bias
the instantaneous value of the bias potentialmetaD_phi2_3: 
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
=phi2_3 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_phi2_3
The METAD action with label metaD_phi2_3 calculates the following quantities:
 Quantity   
 Description  
metaD_phi2_3.bias
the instantaneous value of the bias potentialmetaD_psi2_3: 
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
=psi2_3 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_psi2_3
#
The METAD action with label metaD_psi2_3 calculates the following quantities:
 Quantity   
 Description  
metaD_psi2_3.bias
the instantaneous value of the bias potentialmetaD_phi3_4: 
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
=phi3_4 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_phi3_4
The METAD action with label metaD_phi3_4 calculates the following quantities:
 Quantity   
 Description  
metaD_phi3_4.bias
the instantaneous value of the bias potentialmetaD_psi3_4: 
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
=psi3_4 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_psi3_4
#
The METAD action with label metaD_psi3_4 calculates the following quantities:
 Quantity   
 Description  
metaD_psi3_4.bias
the instantaneous value of the bias potentialmetaD_phi3_5: 
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
=phi3_5 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_phi3_5
The METAD action with label metaD_phi3_5 calculates the following quantities:
 Quantity   
 Description  
metaD_phi3_5.bias
the instantaneous value of the bias potentialmetaD_psi3_5: 
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
=psi3_5 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_psi3_5
The METAD action with label metaD_psi3_5 calculates the following quantities:
 Quantity   
 Description  
metaD_psi3_5.bias
the instantaneous value of the bias potentialmetaD_omega3_5: 
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
=omega3_5 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_omega3_5
#
The METAD action with label metaD_omega3_5 calculates the following quantities:
 Quantity   
 Description  
metaD_omega3_5.bias
the instantaneous value of the bias potentialmetaD_phi5_6: 
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
=phi5_6 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_phi5_6
The METAD action with label metaD_phi5_6 calculates the following quantities:
 Quantity   
 Description  
metaD_phi5_6.bias
the instantaneous value of the bias potentialmetaD_psi5_6: 
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
=psi5_6 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_psi5_6
#
The METAD action with label metaD_psi5_6 calculates the following quantities:
 Quantity   
 Description  
metaD_psi5_6.bias
the instantaneous value of the bias potentialmetaD_phi5_7: 
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
=phi5_7 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_phi5_7
The METAD action with label metaD_phi5_7 calculates the following quantities:
 Quantity   
 Description  
metaD_phi5_7.bias
the instantaneous value of the bias potentialmetaD_psi5_7: 
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
=psi5_7 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_psi5_7
The METAD action with label metaD_psi5_7 calculates the following quantities:
 Quantity   
 Description  
metaD_psi5_7.bias
the instantaneous value of the bias potentialmetaD_omega5_7: 
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
=omega5_7 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_omega5_7
#
The METAD action with label metaD_omega5_7 calculates the following quantities:
 Quantity   
 Description  
metaD_omega5_7.bias
the instantaneous value of the bias potentialmetaD_phi1_8: 
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
=phi1_8 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_phi1_8
The METAD action with label metaD_phi1_8 calculates the following quantities:
 Quantity   
 Description  
metaD_phi1_8.bias
the instantaneous value of the bias potentialmetaD_psi1_8: 
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
=psi1_8 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_psi1_8
The METAD action with label metaD_psi1_8 calculates the following quantities:
 Quantity   
 Description  
metaD_psi1_8.bias
the instantaneous value of the bias potentialmetaD_omega1_8: 
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
=omega1_8 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=4.0 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.35 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
GRID_BIN
the number of bins for the grid
=200 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15 
RECT
list of bias factors for all the replicas
=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14 
FILE
 a file in which the list of added hills is stored
=HILLS_omega1_8
#
# PRINT torsion angle values and puckering coordinates to separate files
#
The METAD action with label metaD_omega1_8 calculates the following quantities:
 Quantity   
 Description  
metaD_omega1_8.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=phi1_2,psi1_2,phi2_3,psi2_3,phi3_4,psi3_4,phi3_5,psi3_5,omega3_5,phi5_6,psi5_6,phi5_7,psi5_7,omega5_7,phi1_8,psi1_8,omega1_8 
STRIDE
 the frequency with which the quantities of interest should be output
=200 
FILE
the name of the file on which to output these quantities
=COLVAR
#
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=puck1.theta,puck2.theta,puck3.theta,puck4.theta,puck5.theta,puck6.theta,puck7.theta,puck8.theta,puck1.phi,puck2.phi,puck3.phi,puck4.phi,puck5.phi,puck6.phi,puck7.phi,puck8.phi 
STRIDE
 the frequency with which the quantities of interest should be output
=200 
FILE
the name of the file on which to output these quantities
=COLVAR_theta