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 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 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.