PLUMED-NEST-TEST-SITE

Project ID: plumID:25.007
Source: plumed_M5G0_restrain.dat
Originally used with PLUMED version: 2.8
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

RESTARTActivate restart. More details
The RESTART action with label  calculates somethingMOLINFOThis 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_M5G0_restrain.pdb
# selection of torsion angles and rings
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phi1_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. ,@O6-2the O6 atom in residue 2. Click here for more information. ,@C6-2the C6 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. ,@O6-2the O6 atom in residue 2. Click here for more information. ,@C6-2the C6 atom in residue 2. Click here for more information. ,@C5-2the C5 atom in residue 2. Click here for more information. 
omega2_3The TORSION action with label omega2_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega2_3
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@O6-2the O6 atom in residue 2. Click here for more information. ,@C6-2the C6 atom in residue 2. Click here for more information. ,@C5-2the C5 atom in residue 2. Click here for more information. ,@O5-2the O5 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. 
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phi3_5The TORSION action with label phi3_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3_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. ,@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_5The TORSION action with label psi3_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3_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. ,@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_5The TORSION action with label omega3_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega3_5
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. 
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phi2_6The TORSION action with label phi2_6 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2_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. ,@O3-2the O3 atom in residue 2. Click here for more information. ,@C3-2the C3 atom in residue 2. Click here for more information. 
psi2_6The TORSION action with label psi2_6 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2_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. ,@O3-2the O3 atom in residue 2. Click here for more information. ,@C3-2the C3 atom in residue 2. Click here for more information. ,@C2-2the C2 atom in residue 2. Click here for more information. 
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phi6_7The TORSION action with label phi6_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi6_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. ,@O2-6the O2 atom in residue 6. Click here for more information. ,@C2-6the C2 atom in residue 6. Click here for more information. 
psi6_7The TORSION action with label psi6_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi6_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. ,@O2-6the O2 atom in residue 6. Click here for more information. ,@C2-6the C2 atom in residue 6. Click here for more information. ,@C1-6the C1 atom in residue 6. Click here for more information. 
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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. 
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r_phi1_2The RESTRAINT action with label r_phi1_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_phi1_2.bias
scalar
the instantaneous value of the bias potential
r_phi1_2.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=phi1_2 ATthe position of the restraint=-1.4 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_phi1_2: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=phi1_2 ATthe position of the restraint=-1.4 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
r_psi1_2The RESTRAINT action with label r_psi1_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_psi1_2.bias
scalar
the instantaneous value of the bias potential
r_psi1_2.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=psi1_2 ATthe position of the restraint=1.9 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_psi1_2: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=psi1_2 ATthe position of the restraint=1.9 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
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r_phi2_3The RESTRAINT action with label r_phi2_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_phi2_3.bias
scalar
the instantaneous value of the bias potential
r_phi2_3.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=phi2_3 ATthe position of the restraint=2.8 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_phi2_3: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=phi2_3 ATthe position of the restraint=2.8 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
r_psi2_3The RESTRAINT action with label r_psi2_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_psi2_3.bias
scalar
the instantaneous value of the bias potential
r_psi2_3.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=psi2_3 ATthe position of the restraint=-2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_psi2_3: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=psi2_3 ATthe position of the restraint=-2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
r_omega2_3The RESTRAINT action with label r_omega2_3 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_omega2_3.bias
scalar
the instantaneous value of the bias potential
r_omega2_3.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=omega2_3 ATthe position of the restraint=1.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_omega2_3: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=omega2_3 ATthe position of the restraint=1.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
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r_phi3_4The RESTRAINT action with label r_phi3_4 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_phi3_4.bias
scalar
the instantaneous value of the bias potential
r_phi3_4.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=phi3_4 ATthe position of the restraint=1.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_phi3_4: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=phi3_4 ATthe position of the restraint=1.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
r_psi3_4The RESTRAINT action with label r_psi3_4 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_psi3_4.bias
scalar
the instantaneous value of the bias potential
r_psi3_4.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=psi3_4 ATthe position of the restraint=-1.9 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_psi3_4: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=psi3_4 ATthe position of the restraint=-1.9 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
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r_phi3_5The RESTRAINT action with label r_phi3_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_phi3_5.bias
scalar
the instantaneous value of the bias potential
r_phi3_5.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=phi3_5 ATthe position of the restraint=1.1 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_phi3_5: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=phi3_5 ATthe position of the restraint=1.1 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
r_psi3_5The RESTRAINT action with label r_psi3_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_psi3_5.bias
scalar
the instantaneous value of the bias potential
r_psi3_5.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=psi3_5 ATthe position of the restraint=3.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_psi3_5: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=psi3_5 ATthe position of the restraint=3.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
r_omega3_5The RESTRAINT action with label r_omega3_5 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_omega3_5.bias
scalar
the instantaneous value of the bias potential
r_omega3_5.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=omega3_5 ATthe position of the restraint=-1.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_omega3_5: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=omega3_5 ATthe position of the restraint=-1.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
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r_phi2_6The RESTRAINT action with label r_phi2_6 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_phi2_6.bias
scalar
the instantaneous value of the bias potential
r_phi2_6.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=phi2_6 ATthe position of the restraint=1.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_phi2_6: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=phi2_6 ATthe position of the restraint=1.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
r_psi2_6The RESTRAINT action with label r_psi2_6 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_psi2_6.bias
scalar
the instantaneous value of the bias potential
r_psi2_6.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=psi2_6 ATthe position of the restraint=-2.7 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_psi2_6: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=psi2_6 ATthe position of the restraint=-2.7 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
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r_phi6_7The RESTRAINT action with label r_phi6_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_phi6_7.bias
scalar
the instantaneous value of the bias potential
r_phi6_7.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=phi6_7 ATthe position of the restraint=-1.5 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_phi6_7: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=phi6_7 ATthe position of the restraint=-1.5 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
r_psi6_7The RESTRAINT action with label r_psi6_7 calculates the following quantities:
 Quantity   
 Type   
 Description  
r_psi6_7.bias
scalar
the instantaneous value of the bias potential
r_psi6_7.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=psi6_7 ATthe position of the restraint=-2.4 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50
r_psi6_7: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=psi6_7 ATthe position of the restraint=-2.4 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
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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,omega2_3,phi3_4,psi3_4,phi3_5,psi3_5,omega3_5,phi2_6,psi2_6,phi6_7,psi6_7 STRIDE the frequency with which the quantities of interest should be output=4000 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,puck1.phi,puck2.phi,puck3.phi,puck4.phi,puck5.phi,puck6.phi,puck7.phi STRIDE the frequency with which the quantities of interest should be output=4000 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=*.bias STRIDE the frequency with which the quantities of interest should be output=4000 FILEthe name of the file on which to output these quantities=COLVAR_restraint
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