JCOUPLING

This is part of the colvar module |

Calculates \(^3J\) coupling constants for a dihedral angle.

The J-coupling between two atoms is given by the Karplus relation:

\[ ^3J(\theta)=A\cos^2(\theta+\Delta\theta)+B\cos(\theta+\Delta\theta)+C \]

where \(A\), \(B\) and \(C\) are the Karplus parameters and \(\Delta\theta\) is an additional constant added on to the dihedral angle \(\theta\). The Karplus parameters are determined empirically and are dependent on the type of J-coupling.

This collective variable computes the J-couplings for a set of atoms defining a dihedral angle. You can specify the atoms involved using the MOLINFO notation. You can also specify the experimental couplings using the ADDCOUPLINGS flag and COUPLING keywords. These will be included in the output. You must choose the type of coupling using the type keyword, you can also supply custom Karplus parameters using TYPE=CUSTOM and the A, B, C and SHIFT keywords. You will need to make sure you are using the correct dihedral angle:

- Ha-N: \(\psi\)
- Ha-HN: \(\phi\)
- N-C \(\gamma\): \(\chi_1\)
- CO-C \(\gamma\): \(\chi_1\)

- Description of components

The names of the components in this action can be customized by the user in the actions input file. However, in addition to these customizable components the following quantities will always be output

Quantity | Description |

j | the calculated J-coupling |

In addition the following quantities can be calculated by employing the keywords listed below

Quantity | Keyword | Description |

exp | ADDCOUPLINGS | the experimental J-coupling |

- The atoms involved can be specified using

ATOMS | the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one J-coupling will be calculated for each ATOMS keyword you specify. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3... |

- Compulsory keywords

TYPE | Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM) |

- Options

NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |

NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |

ADDCOUPLINGS | ( default=off ) Set this flag if you want to have fixed components with the experimental values. |

A | Karplus parameter A |

B | Karplus parameter B |

C | Karplus parameter C |

SHIFT | Angle shift in radians |

COUPLING | Add an experimental value for each coupling You can use multiple instances of this keyword i.e. COUPLING1, COUPLING2, COUPLING3... |

- Examples

In the following example we calculate the Ha-N J-coupling from a set of atoms involved in dihedral \(\psi\) angles in the peptide backbone. We also add the experimental datapoints and compute the correlation and other measures and finally print the results.

MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb WHOLEMOLECULES ENTITY0=1-111 JCOUPLING ... ADDCOUPLINGS TYPE=HAN ATOMS1=@psi-2 COUPLING1=-0.49 ATOMS2=@psi-4 COUPLING2=-0.54 ATOMS3=@psi-5 COUPLING3=-0.53 ATOMS4=@psi-7 COUPLING4=-0.39 ATOMS5=@psi-8 COUPLING5=-0.39 LABEL=jhan ... JCOUPLING jhanst: STATS ARG=(jhan\.j_.*) PARARG=(jhan\.exp_.*) PRINT ARG=jhanst.*,jhan.* FILE=COLVAR STRIDE=100 ENDPLUMED