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.

- Examples

The following provides an example input for the DIHCOR action

Click on the labels of the actions for more information on what each action computes

dih:DIHCOR ...ATOMS1=1,2,3,4,5,6,7,8the atoms involved in each of the dihedral correlation values you wish to calculate.ATOMS2=5,6,7,8,9,10,11,12 ... PRINTthe atoms involved in each of the dihedral correlation values you wish to calculate.ARG=the input for this action is the scalar output from one or more other actions.dihFILE=colvarthe name of the file on which to output these quantitiesSTRIDE=10compulsory keyword ( default=1 )the frequency with which the quantities of interest should be output

In the above input we are calculating the correlation 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 between 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 torsion angles 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:

Click on the labels of the actions for more information on what each action computes

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb MOLINFOMOLTYPE=proteincompulsory keyword ( default=protein )what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleSTRUCTURE=myprotein.pdbcompulsory keyworda file in pdb format containing a reference structure.dih:DIHCOR ...ATOMS1=@phi-3,@psi-3the atoms involved in each of the dihedral correlation values you wish to calculate.ATOMS2=@psi-3,@phi-4the atoms involved in each of the dihedral correlation values you wish to calculate.ATOMS3=@phi-4,@psi-4 ... PRINTthe atoms involved in each of the dihedral correlation values you wish to calculate.ARG=the input for this action is the scalar output from one or more other actions.dihFILE=colvarthe name of the file on which to output these quantitiesSTRIDE=10compulsory keyword ( default=1 )the frequency with which the quantities of interest should be output

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 fourth residue of the protein.

- Glossary of keywords and components

- The atoms involved can be specified using

ATOMS | the atoms involved in each of the dihedral correlation values you wish to calculate. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one dihedral correlation will be calculated for each ATOM keyword you specify (all ATOM keywords should specify the indices of 8 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 use MPI |

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

TIMINGS | ( default=off ) output information on the timings of the various parts of the calculation |