DIHCOR

This is part of the multicolvar module |

Measures the degree of similarity between dihedral angles.

This colvar calculates the following quantity.

\[ s = \frac{1}{2} \sum_i \left[ 1 + \cos( \phi_i - \psi_i ) \right] \]

where the \(\phi_i\) and \(\psi\) values and the instantaneous values for the TORSION angles of interest.

- The atoms involved can be specified using

ATOMS | the atoms involved in each of the collective variables you wish to calculate. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one CV will be calculated for each ATOM keyword you specify (all ATOM keywords should define the same number of atoms). The eventual number of quantities calculated by this action will depend on what functions of the distribution you choose to calculate. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3... |

- Options

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

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

SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |

LOWMEM | ( default=off ) lower the memory requirements |

VERBOSE | ( default=off ) write a more detailed output |

TOL | this keyword can be used to speed up your calculation. When accumulating sums in which the individual terms are numbers inbetween zero and one it is assumed that terms less than a certain tolerance make only a small contribution to the sum. They can thus be safely ignored as can the the derivatives wrt these small quantities. |

- Examples

The following provides an example input for the dihcor action

DIHCOR ... ATOMS1=1,2,3,4,5,6,7,8 ATOMS2=5,6,7,8,9,10,11,12 LABEL=dih ... DIHCOR PRINT ARG=dih FILE=colvar STRIDE=10

In the above input we are calculating the correation between the torsion angle involving atoms 1, 2, 3 and 4 and the torsion angle involving atoms 5, 6, 7 and 8. This is then added to the correlation betwene the torsion angle involving atoms 5, 6, 7 and 8 and the correlation angle involving atoms 9, 10, 11 and 12.

Writing out the atoms involved in all the torsions in this way can be rather tedious. Thankfully if you are working with protein you can avoid this by using the MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:

MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb DIHCOR ... ATOMS1=@phi-3,@psi-3 ATOMS2=@psi-3,@phi-4 ATOMS4=@phi-4,@psi-4 ... DIHCOR PRINT ARG=dih FILE=colvar STRIDE=10

Here, @phi-3 tells plumed that you would like to calculate the \(\phi\) angle in the third residue of the protein. Similarly @psi-4 tells plumed that you want to calculate the \(\psi\) angle of the 4th residue of the protein.