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
the atoms involved in each of the alpha-beta variables you wish to calculate. 
=168,170,172,188 
REFERENCE1
compulsory keyword 
the reference values for each of the torsional angles. 
=3.14 
   
ATOMS2
the atoms involved in each of the alpha-beta variables you wish to calculate. 
=170,172,188,190 
REFERENCE2
compulsory keyword 
the reference values for each of the torsional angles. 
=3.14 
   
ATOMS3
the atoms involved in each of the alpha-beta variables you wish to calculate. 
=188,190,192,230 
REFERENCE3
compulsory keyword 
the reference values for each of the torsional angles. 
=3.14 
   
...The ALPHABETA action with label ab calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=ab 
FILE
the name of the file on which to output these quantities 
=colvar 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=10 The PRINT action with label 

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
the atoms involved in each of the alpha-beta variables you wish to calculate. 
=168,170,172,188 
REFERENCE
compulsory keyword 
the reference values for each of the torsional angles. 
=3.14 
   
ATOMS2
the atoms involved in each of the alpha-beta variables you wish to calculate. 
=170,172,188,190 
   
ATOMS3
the atoms involved in each of the alpha-beta variables you wish to calculate. 
=188,190,192,230 
   
...The ALPHABETA action with label ab calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=ab 
FILE
the name of the file on which to output these quantities 
=colvar 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=10 The PRINT action with label 

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
MOLINFO 
MOLTYPE
compulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible 
=protein 
STRUCTURE
compulsory keyword 
a file in pdb format containing a reference structure. 
=myprotein.pdb The MOLINFO action with label 
ab: ALPHABETA ...
   
ATOMS1
the atoms involved in each of the alpha-beta variables you wish to calculate. 
=@phi-3 
REFERENCE
compulsory keyword 
the reference values for each of the torsional angles. 
=3.14 
   
ATOMS2
the atoms involved in each of the alpha-beta variables you wish to calculate. 
=@psi-3 
   
ATOMS3
the atoms involved in each of the alpha-beta variables you wish to calculate. 
=@phi-4 
   
...The ALPHABETA action with label ab calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=ab 
FILE
the name of the file on which to output these quantities 
=colvar 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=10 The PRINT action with label 

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...