PLUMED-NEST-TEST-SITE

Project ID: plumID:22.028
Source: plumed_M9.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 #########
#
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=reference_M9.pdb
#
# Define torsion angles for M9
#
The MOLINFO action with label  calculates somethingphi1_2The TORSION action with label phi1_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi1_2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-2the O5 atom in residue 2. Click here for more information. ,@C1-2the C1 atom in residue 2. Click here for more information. ,@O4-1the O4 atom in residue 1. Click here for more information. ,@C4-1the C4 atom in residue 1. Click here for more information. 
psi1_2The TORSION action with label psi1_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi1_2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-2the C1 atom in residue 2. Click here for more information. ,@O4-1the O4 atom in residue 1. Click here for more information. ,@C4-1the C4 atom in residue 1. Click here for more information. ,@C3-1the C3 atom in residue 1. Click here for more information. 
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phi2_3The TORSION action with label phi2_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2_3
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-3the O5 atom in residue 3. Click here for more information. ,@C1-3the C1 atom in residue 3. Click here for more information. ,@O4-2the O4 atom in residue 2. Click here for more information. ,@C4-2the C4 atom in residue 2. Click here for more information. 
psi2_3The TORSION action with label psi2_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2_3
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-3the C1 atom in residue 3. Click here for more information. ,@O4-2the O4 atom in residue 2. Click here for more information. ,@C4-2the C4 atom in residue 2. Click here for more information. ,@C3-2the C3 atom in residue 2. Click here for more information. 
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phi3_4The TORSION action with label phi3_4 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3_4
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-4the O5 atom in residue 4. Click here for more information. ,@C1-4the C1 atom in residue 4. Click here for more information. ,@O3-3the O3 atom in residue 3. Click here for more information. ,@C3-3the C3 atom in residue 3. Click here for more information. 
psi3_4The TORSION action with label psi3_4 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3_4
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-4the C1 atom in residue 4. Click here for more information. ,@O3-3the O3 atom in residue 3. Click here for more information. ,@C3-3the C3 atom in residue 3. Click here for more information. ,@C2-3the C2 atom in residue 3. Click here for more information. 
#
phi4_5The TORSION action with label phi4_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi4_5
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-5the O5 atom in residue 5. Click here for more information. ,@C1-5the C1 atom in residue 5. Click here for more information. ,@O2-4the O2 atom in residue 4. Click here for more information. ,@C2-4the C2 atom in residue 4. Click here for more information. 
psi4_5The TORSION action with label psi4_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi4_5
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-5the C1 atom in residue 5. Click here for more information. ,@O2-4the O2 atom in residue 4. Click here for more information. ,@C2-4the C2 atom in residue 4. Click here for more information. ,@C1-4the C1 atom in residue 4. Click here for more information. 
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phi5_6The TORSION action with label phi5_6 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi5_6
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-6the O5 atom in residue 6. Click here for more information. ,@C1-6the C1 atom in residue 6. Click here for more information. ,@O2-5the O2 atom in residue 5. Click here for more information. ,@C2-5the C2 atom in residue 5. Click here for more information. 
psi5_6The TORSION action with label psi5_6 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi5_6
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-6the C1 atom in residue 6. Click here for more information. ,@O2-5the O2 atom in residue 5. Click here for more information. ,@C2-5the C2 atom in residue 5. Click here for more information. ,@C1-5the C1 atom in residue 5. Click here for more information. 

phi3_7The TORSION action with label phi3_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3_7
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-7the O5 atom in residue 7. Click here for more information. ,@C1-7the C1 atom in residue 7. Click here for more information. ,@O6-3the O6 atom in residue 3. Click here for more information. ,@C6-3the C6 atom in residue 3. Click here for more information. 
psi3_7The TORSION action with label psi3_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3_7
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-7the C1 atom in residue 7. Click here for more information. ,@O6-3the O6 atom in residue 3. Click here for more information. ,@C6-3the C6 atom in residue 3. Click here for more information. ,@C5-3the C5 atom in residue 3. Click here for more information. 
omega3_7The TORSION action with label omega3_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega3_7
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O6-3the O6 atom in residue 3. Click here for more information. ,@C6-3the C6 atom in residue 3. Click here for more information. ,@C5-3the C5 atom in residue 3. Click here for more information. ,@O5-3the O5 atom in residue 3. Click here for more information. 
#
phi7_8The TORSION action with label phi7_8 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi7_8
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-8the O5 atom in residue 8. Click here for more information. ,@C1-8the C1 atom in residue 8. Click here for more information. ,@O3-7the O3 atom in residue 7. Click here for more information. ,@C3-7the C3 atom in residue 7. Click here for more information. 
psi7_8The TORSION action with label psi7_8 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi7_8
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-8the C1 atom in residue 8. Click here for more information. ,@O3-7the O3 atom in residue 7. Click here for more information. ,@C3-7the C3 atom in residue 7. Click here for more information. ,@C2-7the C2 atom in residue 7. Click here for more information. 
#
phi8_9The TORSION action with label phi8_9 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi8_9
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-9the O5 atom in residue 9. Click here for more information. ,@C1-9the C1 atom in residue 9. Click here for more information. ,@O2-8the O2 atom in residue 8. Click here for more information. ,@C2-8the C2 atom in residue 8. Click here for more information. 
psi8_9The TORSION action with label psi8_9 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi8_9
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-9the C1 atom in residue 9. Click here for more information. ,@O2-8the O2 atom in residue 8. Click here for more information. ,@C2-8the C2 atom in residue 8. Click here for more information. ,@C1-8the C1 atom in residue 8. Click here for more information. 
#
phi7_10The TORSION action with label phi7_10 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi7_10
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-10the O5 atom in residue 10. Click here for more information. ,@C1-10the C1 atom in residue 10. Click here for more information. ,@O6-7the O6 atom in residue 7. Click here for more information. ,@C6-7the C6 atom in residue 7. Click here for more information. 
psi7_10The TORSION action with label psi7_10 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi7_10
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-10the C1 atom in residue 10. Click here for more information. ,@O6-7the O6 atom in residue 7. Click here for more information. ,@C6-7the C6 atom in residue 7. Click here for more information. ,@C5-7the C5 atom in residue 7. Click here for more information. 
omega7_10The TORSION action with label omega7_10 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega7_10
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O6-7the O6 atom in residue 7. Click here for more information. ,@C6-7the C6 atom in residue 7. Click here for more information. ,@C5-7the C5 atom in residue 7. Click here for more information. ,@O5-7the O5 atom in residue 7. Click here for more information. 
#
phi10_11The TORSION action with label phi10_11 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi10_11
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O5-11the O5 atom in residue 11. Click here for more information. ,@C1-11the C1 atom in residue 11. Click here for more information. ,@O2-10the O2 atom in residue 10. Click here for more information. ,@C2-10the C2 atom in residue 10. Click here for more information. 
psi10_11The TORSION action with label psi10_11 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi10_11
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@C1-11the C1 atom in residue 11. Click here for more information. ,@O2-10the O2 atom in residue 10. Click here for more information. ,@C2-10the C2 atom in residue 10. Click here for more information. ,@C1-10the C1 atom in residue 10. Click here for more information. 
#
# Define puckering for each monosaccharide only to print it to file
#
puck1The PUCKERING action with label puck1 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck1.qx
scalar
Cartesian component x (6 membered rings)
puck1.qy
scalar
Cartesian component y (6 membered rings)
puck1.qz
scalar
Cartesian component z (6 membered rings)
puck1.phi
scalar
Pseudorotation phase (6 membered rings)
puck1.theta
scalar
Theta angle (6 membered rings)
puck1.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-1the O5 atom in residue 1. Click here for more information. ,@C1-1the C1 atom in residue 1. Click here for more information. ,@C2-1the C2 atom in residue 1. Click here for more information. ,@C3-1the C3 atom in residue 1. Click here for more information. ,@C4-1the C4 atom in residue 1. Click here for more information. ,@C5-1the C5 atom in residue 1. Click here for more information. 
puck2The PUCKERING action with label puck2 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck2.qx
scalar
Cartesian component x (6 membered rings)
puck2.qy
scalar
Cartesian component y (6 membered rings)
puck2.qz
scalar
Cartesian component z (6 membered rings)
puck2.phi
scalar
Pseudorotation phase (6 membered rings)
puck2.theta
scalar
Theta angle (6 membered rings)
puck2.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-2the O5 atom in residue 2. Click here for more information. ,@C1-2the C1 atom in residue 2. Click here for more information. ,@C2-2the C2 atom in residue 2. Click here for more information. ,@C3-2the C3 atom in residue 2. Click here for more information. ,@C4-2the C4 atom in residue 2. Click here for more information. ,@C5-2the C5 atom in residue 2. Click here for more information. 
puck3The PUCKERING action with label puck3 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck3.qx
scalar
Cartesian component x (6 membered rings)
puck3.qy
scalar
Cartesian component y (6 membered rings)
puck3.qz
scalar
Cartesian component z (6 membered rings)
puck3.phi
scalar
Pseudorotation phase (6 membered rings)
puck3.theta
scalar
Theta angle (6 membered rings)
puck3.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-3the O5 atom in residue 3. Click here for more information. ,@C1-3the C1 atom in residue 3. Click here for more information. ,@C2-3the C2 atom in residue 3. Click here for more information. ,@C3-3the C3 atom in residue 3. Click here for more information. ,@C4-3the C4 atom in residue 3. Click here for more information. ,@C5-3the C5 atom in residue 3. Click here for more information. 
puck4The PUCKERING action with label puck4 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck4.qx
scalar
Cartesian component x (6 membered rings)
puck4.qy
scalar
Cartesian component y (6 membered rings)
puck4.qz
scalar
Cartesian component z (6 membered rings)
puck4.phi
scalar
Pseudorotation phase (6 membered rings)
puck4.theta
scalar
Theta angle (6 membered rings)
puck4.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-4the O5 atom in residue 4. Click here for more information. ,@C1-4the C1 atom in residue 4. Click here for more information. ,@C2-4the C2 atom in residue 4. Click here for more information. ,@C3-4the C3 atom in residue 4. Click here for more information. ,@C4-4the C4 atom in residue 4. Click here for more information. ,@C5-4the C5 atom in residue 4. Click here for more information. 
puck5The PUCKERING action with label puck5 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck5.qx
scalar
Cartesian component x (6 membered rings)
puck5.qy
scalar
Cartesian component y (6 membered rings)
puck5.qz
scalar
Cartesian component z (6 membered rings)
puck5.phi
scalar
Pseudorotation phase (6 membered rings)
puck5.theta
scalar
Theta angle (6 membered rings)
puck5.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-5the O5 atom in residue 5. Click here for more information. ,@C1-5the C1 atom in residue 5. Click here for more information. ,@C2-5the C2 atom in residue 5. Click here for more information. ,@C3-5the C3 atom in residue 5. Click here for more information. ,@C4-5the C4 atom in residue 5. Click here for more information. ,@C5-5the C5 atom in residue 5. Click here for more information. 
puck6The PUCKERING action with label puck6 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck6.qx
scalar
Cartesian component x (6 membered rings)
puck6.qy
scalar
Cartesian component y (6 membered rings)
puck6.qz
scalar
Cartesian component z (6 membered rings)
puck6.phi
scalar
Pseudorotation phase (6 membered rings)
puck6.theta
scalar
Theta angle (6 membered rings)
puck6.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-6the O5 atom in residue 6. Click here for more information. ,@C1-6the C1 atom in residue 6. Click here for more information. ,@C2-6the C2 atom in residue 6. Click here for more information. ,@C3-6the C3 atom in residue 6. Click here for more information. ,@C4-6the C4 atom in residue 6. Click here for more information. ,@C5-6the C5 atom in residue 6. Click here for more information. 
puck7The PUCKERING action with label puck7 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck7.qx
scalar
Cartesian component x (6 membered rings)
puck7.qy
scalar
Cartesian component y (6 membered rings)
puck7.qz
scalar
Cartesian component z (6 membered rings)
puck7.phi
scalar
Pseudorotation phase (6 membered rings)
puck7.theta
scalar
Theta angle (6 membered rings)
puck7.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-7the O5 atom in residue 7. Click here for more information. ,@C1-7the C1 atom in residue 7. Click here for more information. ,@C2-7the C2 atom in residue 7. Click here for more information. ,@C3-7the C3 atom in residue 7. Click here for more information. ,@C4-7the C4 atom in residue 7. Click here for more information. ,@C5-7the C5 atom in residue 7. Click here for more information. 
puck8The PUCKERING action with label puck8 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck8.qx
scalar
Cartesian component x (6 membered rings)
puck8.qy
scalar
Cartesian component y (6 membered rings)
puck8.qz
scalar
Cartesian component z (6 membered rings)
puck8.phi
scalar
Pseudorotation phase (6 membered rings)
puck8.theta
scalar
Theta angle (6 membered rings)
puck8.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-8the O5 atom in residue 8. Click here for more information. ,@C1-8the C1 atom in residue 8. Click here for more information. ,@C2-8the C2 atom in residue 8. Click here for more information. ,@C3-8the C3 atom in residue 8. Click here for more information. ,@C4-8the C4 atom in residue 8. Click here for more information. ,@C5-8the C5 atom in residue 8. Click here for more information. 
puck9The PUCKERING action with label puck9 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck9.qx
scalar
Cartesian component x (6 membered rings)
puck9.qy
scalar
Cartesian component y (6 membered rings)
puck9.qz
scalar
Cartesian component z (6 membered rings)
puck9.phi
scalar
Pseudorotation phase (6 membered rings)
puck9.theta
scalar
Theta angle (6 membered rings)
puck9.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-9the O5 atom in residue 9. Click here for more information. ,@C1-9the C1 atom in residue 9. Click here for more information. ,@C2-9the C2 atom in residue 9. Click here for more information. ,@C3-9the C3 atom in residue 9. Click here for more information. ,@C4-9the C4 atom in residue 9. Click here for more information. ,@C5-9the C5 atom in residue 9. Click here for more information. 
puck10The PUCKERING action with label puck10 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck10.qx
scalar
Cartesian component x (6 membered rings)
puck10.qy
scalar
Cartesian component y (6 membered rings)
puck10.qz
scalar
Cartesian component z (6 membered rings)
puck10.phi
scalar
Pseudorotation phase (6 membered rings)
puck10.theta
scalar
Theta angle (6 membered rings)
puck10.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-10the O5 atom in residue 10. Click here for more information. ,@C1-10the C1 atom in residue 10. Click here for more information. ,@C2-10the C2 atom in residue 10. Click here for more information. ,@C3-10the C3 atom in residue 10. Click here for more information. ,@C4-10the C4 atom in residue 10. Click here for more information. ,@C5-10the C5 atom in residue 10. Click here for more information. 
puck11The PUCKERING action with label puck11 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck11.qx
scalar
Cartesian component x (6 membered rings)
puck11.qy
scalar
Cartesian component y (6 membered rings)
puck11.qz
scalar
Cartesian component z (6 membered rings)
puck11.phi
scalar
Pseudorotation phase (6 membered rings)
puck11.theta
scalar
Theta angle (6 membered rings)
puck11.amplitude
scalar
Pseudorotation amplitude (6 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@O5-11the O5 atom in residue 11. Click here for more information. ,@C1-11the C1 atom in residue 11. Click here for more information. ,@C2-11the C2 atom in residue 11. Click here for more information. ,@C3-11the C3 atom in residue 11. Click here for more information. ,@C4-11the C4 atom in residue 11. Click here for more information. ,@C5-11the C5 atom in residue 11. Click here for more information. 
#
# Define torsion angles required for J-coupling calculations
#
J3_7The TORSION action with label J3_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
J3_7
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@H5-3the H5 atom in residue 3. Click here for more information. ,@C5-3the C5 atom in residue 3. Click here for more information. ,@C6-3the C6 atom in residue 3. Click here for more information. ,@H61-3the H61 atom in residue 3. Click here for more information. 
J3_7PThe TORSION action with label J3_7P calculates the following quantities:
 Quantity   
 Type   
 Description  
J3_7P
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@H5-3the H5 atom in residue 3. Click here for more information. ,@C5-3the C5 atom in residue 3. Click here for more information. ,@C6-3the C6 atom in residue 3. Click here for more information. ,@H62-3the H62 atom in residue 3. Click here for more information. 
#
J7_10The TORSION action with label J7_10 calculates the following quantities:
 Quantity   
 Type   
 Description  
J7_10
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@H5-7the H5 atom in residue 7. Click here for more information. ,@C5-7the C5 atom in residue 7. Click here for more information. ,@C6-7the C6 atom in residue 7. Click here for more information. ,@H61-7the H61 atom in residue 7. Click here for more information. 
J7_10PThe TORSION action with label J7_10P calculates the following quantities:
 Quantity   
 Type   
 Description  
J7_10P
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@H5-7the H5 atom in residue 7. Click here for more information. ,@C5-7the C5 atom in residue 7. Click here for more information. ,@C6-7the C6 atom in residue 7. Click here for more information. ,@H62-7the H62 atom in residue 7. 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. 
#
metaD_phi1_2The METAD action with label metaD_phi1_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi1_2.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi1_2 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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
metaD_psi1_2The METAD action with label metaD_psi1_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi1_2.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi1_2 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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
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metaD_phi2_3The METAD action with label metaD_phi2_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi2_3.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi2_3 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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
metaD_psi2_3The METAD action with label metaD_psi2_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi2_3.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi2_3 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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
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metaD_phi3_4The METAD action with label metaD_phi3_4 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi3_4.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi3_4 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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
metaD_psi3_4The METAD action with label metaD_psi3_4 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi3_4.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi3_4 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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
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metaD_phi4_5The METAD action with label metaD_phi4_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi4_5.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi4_5 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_phi4_5
metaD_psi4_5The METAD action with label metaD_psi4_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi4_5.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi4_5 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_psi4_5
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metaD_phi5_6The METAD action with label metaD_phi5_6 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi5_6.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi5_6 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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
metaD_psi5_6The METAD action with label metaD_psi5_6 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi5_6.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi5_6 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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
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metaD_phi3_7The METAD action with label metaD_phi3_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi3_7.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi3_7 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_7
metaD_psi3_7The METAD action with label metaD_psi3_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi3_7.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi3_7 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_7
metaD_omega3_7The METAD action with label metaD_omega3_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_omega3_7.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=omega3_7 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_7
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metaD_phi7_8The METAD action with label metaD_phi7_8 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi7_8.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi7_8 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_phi7_8
metaD_psi7_8The METAD action with label metaD_psi7_8 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi7_8.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi7_8 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_psi7_8
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metaD_phi8_9The METAD action with label metaD_phi8_9 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi8_9.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi8_9 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_phi8_9
metaD_psi8_9The METAD action with label metaD_psi8_9 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi8_9.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi8_9 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_psi8_9
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metaD_phi7_10The METAD action with label metaD_phi7_10 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi7_10.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi7_10 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_phi7_10
metaD_psi7_10The METAD action with label metaD_psi7_10 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi7_10.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi7_10 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_psi7_10
metaD_omega7_10The METAD action with label metaD_omega7_10 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_omega7_10.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=omega7_10 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_omega7_10
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metaD_phi10_11The METAD action with label metaD_phi10_11 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_phi10_11.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=phi10_11 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_phi10_11
metaD_psi10_11The METAD action with label metaD_psi10_11 calculates the following quantities:
 Quantity   
 Type   
 Description  
metaD_psi10_11.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=psi10_11 TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.35 GRID_MINthe lower bounds for the grid=-pi GRID_MAXthe upper bounds for the grid=pi GRID_BINthe number of bins for the grid=200 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15 RECTlist 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_psi10_11
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# PRINT torsion angle values and puckering coordinates to separate files
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PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=phi1_2,psi1_2,phi2_3,psi2_3,phi3_4,psi3_4,phi4_5,psi4_5,phi5_6,psi5_6,phi3_7,psi3_7,omega3_7,phi7_8,psi7_8,phi8_9,psi8_9,phi7_10,psi7_10,omega7_10,phi10_11,psi10_11 STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=COLVAR
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PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=puck1.theta,puck2.theta,puck3.theta,puck4.theta,puck5.theta,puck6.theta,puck7.theta,puck8.theta,puck9.theta,puck10.theta,puck11.theta,puck1.phi,puck2.phi,puck3.phi,puck4.phi,puck5.phi,puck6.phi,puck7.phi,puck8.phi,puck9.phi,puck10.phi,puck11.phi STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=COLVAR_theta
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PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=omega3_7,J3_7,J3_7P,omega7_10,J7_10,J7_10P STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=COLVAR_NMR
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