ALPHABETA

This is part of the multicolvar module |

Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values.

This colvar calculates the following quantity.

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

where the \(\phi_i\) values are the instantaneous values for the TORSION angles of interest. The \(\phi_i^{\textrm{Ref}}\) values are the user-specified reference values for the torsional angles.

- 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... |

- Compulsory keywords

REFERENCE | the reference values for each of the torsional angles. If you use a single REFERENCE value the same reference value is used for all torsions You can use multiple instances of this keyword i.e. REFERENCE1, REFERENCE2, REFERENCE3... |

- 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 |

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

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

- Examples

The following provides an example of the input for an alpha beta similarity.

ALPHABETA ... ATOMS1=168,170,172,188 REFERENCE1=3.14 ATOMS2=170,172,188,190 REFERENCE2=3.14 ATOMS3=188,190,192,230 REFERENCE3=3.14 LABEL=ab ... ALPHABETA PRINT ARG=ab FILE=colvar STRIDE=10

Because all the reference values are the same we can calculate the same quantity using

ALPHABETA ... ATOMS1=168,170,172,188 REFERENCE=3.14 ATOMS2=170,172,188,190 ATOMS3=188,190,192,230 LABEL=ab ... ALPHABETA PRINT ARG=ab FILE=colvar STRIDE=10

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 ALPHABETA ... ATOMS1=@phi-3 REFERENCE=3.14 ATOMS2=@psi-3 ATOMS3=@phi-4 LABEL=ab ... ALPHABETA PRINT ARG=ab 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.