Shortcut: DIHCOR

Module	multicolvar
Description	Usage
Measures the degree of similarity between dihedral angles.
output value	type
the sum of all the dihedral correlations	scalar

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

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 are the instantaneous values for the TORSION angles of interest.

You can see an example input for the DIHCOR action below

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

DIHCORMeasures the degree of similarity between dihedral angles. This action is a shortcut. More details ...
  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
  LABELa label for the action so that its output can be referenced in the input to other actions=dihThe DIHCOR action with label dih calculates the following quantities:
 Quantity   
 Type   
 Description  
dih
scalar
the sum of all the dihedral correlations
... DIHCOR
# PLUMED interprets the command:
# DIHCOR ...
#   ATOMS1=1,2,3,4,5,6,7,8
#   ATOMS2=5,6,7,8,9,10,11,12
#   LABEL=dih
# ... DIHCOR
# as follows (Click the red comment above to revert to the short version of the input):
dih_dataThe DIHEDRAL_CORRELATION action with label dih_data calculates the following quantities:
 Quantity   
 Type   
 Description  
dih_data
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=5,6,7,8,9,10,11,12
dihThe SUM action with label dih calculates the following quantities:
 Quantity   
 Type   
 Description  
dih
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=dih_data PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dih FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=10

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

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=
regtest/basic/rt32/helix.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt32/helix.pdb
    
ATOM      1 HH31 ACE     1      -9.105  -2.402  21.804  0.00  0.00            
ATOM      2  CH3 ACE     1      -8.930  -3.352  22.308  0.00  0.00            
ATOM      3 HH32 ACE     1      -9.504  -3.501  23.223  0.00  0.00            
ATOM      4 HH33 ACE     1      -9.067  -4.173  21.604  0.00  0.00            
ATOM      5  C   ACE     1      -7.450  -3.303  22.659  0.00  0.00            
...
ATOM    129  CH3 NME    14      -1.690  -7.089  20.487  0.00  0.00            
ATOM    130 HH31 NME    14      -1.873  -6.629  21.459  0.00  0.00            
ATOM    131 HH32 NME    14      -1.152  -6.284  19.986  0.00  0.00            
ATOM    132 HH33 NME    14      -1.135  -8.020  20.602  0.00  0.00            
END
  
The MOLINFO action with label  calculates somethingdihThe DIHCOR action with label dih calculates the following quantities:
 Quantity   
 Type   
 Description  
dih
scalar
the sum of all the dihedral correlations: DIHCORMeasures the degree of similarity between dihedral angles. This action is a shortcut. More details ...
ATOMS1the set of 8 atoms that are being used each of the dihedral correlation values=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. ,@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
ATOMS2the set of 8 atoms that are being used each of the dihedral correlation values=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. ,@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
ATOMS3the set of 8 atoms that are being used each of the dihedral correlation values=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. ,@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
...
# PLUMED interprets the command:
# dih: DIHCOR ...
# ATOMS1=@phi-3,@psi-3
# ATOMS2=@psi-3,@phi-4
# ATOMS3=@phi-4,@psi-4
# ...
# as follows (Click the red comment above to revert to the short version of the input):
dih_dataThe DIHEDRAL_CORRELATION action with label dih_data calculates the following quantities:
 Quantity   
 Type   
 Description  
dih_data
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=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. ,@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.  ATOMS2the set of 8 atoms that are being used to calculate this quantity=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. ,@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.  ATOMS3the set of 8 atoms that are being used to calculate this quantity=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. ,@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
dihThe SUM action with label dih calculates the following quantities:
 Quantity   
 Type   
 Description  
dih
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=dih_data PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dih FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=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 fourth residue of the protein.

Syntax

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