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 ...
   
ATOMS1
the set of 8 atoms that are being used each of the dihedral correlation values. 
=1,2,3,4,5,6,7,8 
   
ATOMS2
the 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 
ARG
the input for this action is the scalar output from one or more other actions. 
=dih 
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 

dih_data: DIHEDRAL_CORRELATION 
ATOMS1
the set of 8 atoms that are being used to calculate this quantity. 
=1,2,3,4,5,6,7,8 
ATOMS2
the 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 
ARG
the input to this function. 
=dih_data 
PERIODIC
compulsory 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 
ARG
the input for this action is the scalar output from one or more other actions. 
=dih 
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 

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 
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 
dih: DIHCOR ...
   
ATOMS1
the set of 8 atoms that are being used each of the dihedral correlation values. 
=@phi-3,@psi-3 
   
ATOMS2
the set of 8 atoms that are being used each of the dihedral correlation values. 
=@psi-3,@phi-4 
   
ATOMS3
the 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 
ARG
the input for this action is the scalar output from one or more other actions. 
=dih 
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 

#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 
dih_data: DIHEDRAL_CORRELATION 
ATOMS1
the set of 8 atoms that are being used to calculate this quantity. 
=@phi-3,@psi-3 
ATOMS2
the set of 8 atoms that are being used to calculate this quantity. 
=@psi-3,@phi-4 
ATOMS3
the 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 
ARG
the input to this function. 
=dih_data 
PERIODIC
compulsory 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 
ARG
the input for this action is the scalar output from one or more other actions. 
=dih 
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 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