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.

- Examples

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

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

ab:ALPHABETA ...ATOMS1=168,170,172,188the atoms involved in each of the alpha-beta variables you wish to calculate.REFERENCE1=3.14compulsory keywordthe reference values for each of the torsional angles.ATOMS2=170,172,188,190the atoms involved in each of the alpha-beta variables you wish to calculate.REFERENCE2=3.14compulsory keywordthe reference values for each of the torsional angles.ATOMS3=188,190,192,230the atoms involved in each of the alpha-beta variables you wish to calculate.REFERENCE3=3.14 ... PRINTcompulsory keywordthe reference values for each of the torsional angles.ARG=the input for this action is the scalar output from one or more other actions.abFILE=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

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

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

ab:ALPHABETA ...ATOMS1=168,170,172,188the atoms involved in each of the alpha-beta variables you wish to calculate.REFERENCE=3.14compulsory keywordthe reference values for each of the torsional angles.ATOMS2=170,172,188,190the atoms involved in each of the alpha-beta variables you wish to calculate.ATOMS3=188,190,192,230 ... PRINTthe atoms involved in each of the alpha-beta variables you wish to calculate.ARG=the input for this action is the scalar output from one or more other actions.abFILE=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

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.ab:ALPHABETA ...ATOMS1=@phi-3the atoms involved in each of the alpha-beta variables you wish to calculate.REFERENCE=3.14compulsory keywordthe reference values for each of the torsional angles.ATOMS2=@psi-3the atoms involved in each of the alpha-beta variables you wish to calculate.ATOMS3=@phi-4 ... PRINTthe atoms involved in each of the alpha-beta variables you wish to calculate.ARG=the input for this action is the scalar output from one or more other actions.abFILE=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 alpha-beta variables you wish to calculate. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one alpha-beta values will be calculated for each ATOM keyword you specify (all ATOM keywords should specify the indices of four 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 torsional angles 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 use MPI |

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

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

COEFFICIENT | the coefficient for each of the torsional angles. If you use a single COEFFICIENT value the same reference value is used for all torsional angles You can use multiple instances of this keyword i.e. COEFFICIENT1, COEFFICIENT2, COEFFICIENT3... |