Action: DIHEDRAL_CORRELATION

Module	colvar
Description	Usage
Measure the correlation between a pair of dihedral angles
output value	type
the DIHEDRAL_CORRELATION for these atoms	scalar/vector

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

Measure the correlation between a pair of dihedral angles

This CV measures the correlation between two dihedral angles, $\phi$ and $\psi$, as follows:

$$s = \frac{1}{2} \left[ 1 + \cos( \phi - \psi ) \right]$$

An example input that computes and calculates this quantity with $\phi$ being the dihedral angle involving atoms 1, 2, 3 and 4 and $\psi$ being the angle involving atoms 7, 8, 9 and 10 is shown below:

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

dThe DIHEDRAL_CORRELATION action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DIHEDRAL_CORRELATION for these atoms: DIHEDRAL_CORRELATIONMeasure the correlation between a pair of dihedral angles More details ATOMSthe set of 8 atoms that are being used to calculate this quantity=1,2,3,4,5,6,7,8
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d FILEthe name of the file on which to output these quantities=colvar

If you want to calculate the dihedral correlations between multiple pairs of dihedral angles using this action you would use an input like this one shown below:

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

dThe DIHEDRAL_CORRELATION action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
vector
the DIHEDRAL_CORRELATION for each set of specified atoms: DIHEDRAL_CORRELATIONMeasure the correlation between a pair of dihedral angles More details ...
  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=9,10,11,12,13,14,15,16
...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d FILEthe name of the file on which to output these quantities=colvar

This input calculates and outputs a two dimensional vector that contains two of these dihedral correlation values. Commands similar to these are used within the DIHCOR shortcut.

Syntax

The following table describes the keywords and options that can be used with this action