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

contract shortcuts

dih: DIHCOR ...
   ATOMS1the set of 8 atoms that are being used each of the dihedral correlation values. =1,2,3,4,5,6,7,8 
   ATOMS2the set of 8 atoms that are being used each of the dihedral correlation values. =5,6,7,8,9,10,11,12 
   
...The DIHCOR action with label dih calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. =dih FILEthe name of the file on which to output these quantities =colvar STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =10 The PRINT action with label 

dih_data: DIHEDRAL_CORRELATION ATOMS1the set of 8 atoms that are being used to calculate this quantity. =1,2,3,4,5,6,7,8 ATOMS2the set of 8 atoms that are being used to calculate this quantity. =5,6,7,8,9,10,11,12 The DIHEDRAL_CORRELATION action with label dih_data calculates a single scalar value
dih: SUM ARGthe input to this function. =dih_data PERIODICcompulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. =NO The SUM action with label dih calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. =dih FILEthe name of the file on which to output these quantities =colvar STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =10 The PRINT action with label 

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

contract shortcuts

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPEcompulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible =protein STRUCTUREcompulsory keyword 
a file in pdb format containing a reference structure. =myprotein.pdb The MOLINFO action with label 
dih: DIHCOR ...
   ATOMS1the set of 8 atoms that are being used each of the dihedral correlation values. =@phi-3,@psi-3 
   ATOMS2the set of 8 atoms that are being used each of the dihedral correlation values. =@psi-3,@phi-4 
   ATOMS3the set of 8 atoms that are being used each of the dihedral correlation values. =@phi-4,@psi-4 
...The DIHCOR action with label dih calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. =dih FILEthe name of the file on which to output these quantities =colvar STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =10 The PRINT action with label 

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPEcompulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible =protein STRUCTUREcompulsory keyword 
a file in pdb format containing a reference structure. =myprotein.pdb The MOLINFO action with label 
dih_data: DIHEDRAL_CORRELATION ATOMS1the set of 8 atoms that are being used to calculate this quantity. =@phi-3,@psi-3 ATOMS2the set of 8 atoms that are being used to calculate this quantity. =@psi-3,@phi-4 ATOMS3the set of 8 atoms that are being used to calculate this quantity. =@phi-4,@psi-4 The DIHEDRAL_CORRELATION action with label dih_data calculates a single scalar value
dih: SUM ARGthe input to this function. =dih_data PERIODICcompulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. =NO The SUM action with label dih calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. =dih FILEthe name of the file on which to output these quantities =colvar STRIDEcompulsory 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

Description of components

Quantity	Description
.#!value	the sum of all the dihedral correlations

The atoms involved can be specified using

ATOMS

the set of 8 atoms that are being used each of the dihedral correlation values. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Options

NOPBC

( default=off ) ignore the periodic boundary conditions when calculating distances