Shortcut: ALPHABETA

Module	multicolvar
Description	Usage
Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values.
output value	type
the alpha beta CV	scalar

Details and examples

Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values.

This shortcut calculates the following quantity.

$$s = \frac{1}{2} \sum_i c_i \left[ 1 + \cos( \phi_i - \phi_i^{\textrm{Ref}} ) \right]$$

where the $\phi_i$ values are the instantaneous values for the TORSION angles of interest. The $\phi_i^{\textrm{Ref}}$ values are reference values for the torsional angles that are specified in the input file.

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

abThe ALPHABETA action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the alpha beta CV: ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=168,170,172,188 REFERENCE1the reference values for each of the torsional angles=3.14
ATOMS2the atoms involved for each of the torsions you wish to calculate=170,172,188,190 REFERENCE2the reference values for each of the torsional angles=3.14
ATOMS3the atoms involved for each of the torsions you wish to calculate=188,190,192,230 REFERENCE3the reference values for each of the torsional angles=3.14
...
# PLUMED interprets the command:
# ab: ALPHABETA ...
# ATOMS1=168,170,172,188 REFERENCE1=3.14
# ATOMS2=170,172,188,190 REFERENCE2=3.14
# ATOMS3=188,190,192,230 REFERENCE3=3.14
# ...
# as follows (Click the red comment above to revert to the short version of the input):
ab_torsionsThe TORSION action with label ab_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details  ATOMS1the four atoms involved in the torsional angle=168,170,172,188 ATOMS2the four atoms involved in the torsional angle=170,172,188,190 ATOMS3the four atoms involved in the torsional angle=188,190,192,230
ab_refThe CONSTANT action with label ab_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=3.14,3.14,3.14
ab_coeffThe CONSTANT action with label ab_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1
ab_combThe COMBINE action with label ab_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_comb
vector
the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab_torsions,ab_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab_cosThe CUSTOM action with label ab_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab_comb,ab_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abThe SUM action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=ab_cos 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=ab 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

Because all the reference values are the same we can also calculate the same quantity using

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

abThe ALPHABETA action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the alpha beta CV: ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=168,170,172,188 REFERENCEthe reference values for each of the torsional angles=3.14
ATOMS2the atoms involved for each of the torsions you wish to calculate=170,172,188,190
ATOMS3the atoms involved for each of the torsions you wish to calculate=188,190,192,230
...
# PLUMED interprets the command:
# ab: ALPHABETA ...
# ATOMS1=168,170,172,188 REFERENCE=3.14
# ATOMS2=170,172,188,190
# ATOMS3=188,190,192,230
# ...
# as follows (Click the red comment above to revert to the short version of the input):
ab_torsionsThe TORSION action with label ab_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details  ATOMS1the four atoms involved in the torsional angle=168,170,172,188 ATOMS2the four atoms involved in the torsional angle=170,172,188,190 ATOMS3the four atoms involved in the torsional angle=188,190,192,230
ab_refThe CONSTANT action with label ab_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=3.14,3.14,3.14
ab_coeffThe CONSTANT action with label ab_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1
ab_combThe COMBINE action with label ab_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_comb
vector
the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab_torsions,ab_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab_cosThe CUSTOM action with label ab_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab_comb,ab_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abThe SUM action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=ab_cos 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=ab 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

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 somethingabThe ALPHABETA action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the alpha beta CV: ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.  REFERENCEthe reference values for each of the torsional angles=3.14 COEFFICIENT1the coefficient for each of the torsional angles=2
ATOMS2the atoms involved for each of the torsions you wish to calculate=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.                 COEFFICIENT2the coefficient for each of the torsional angles=0.5
ATOMS3the atoms involved for each of the torsions you wish to calculate=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.                 COEFFICIENT3the coefficient for each of the torsional angles=1
...
# PLUMED interprets the command:
# ab: ALPHABETA ...
# ATOMS1=@phi-3 REFERENCE=3.14 COEFFICIENT1=2
# ATOMS2=@psi-3                COEFFICIENT2=0.5
# ATOMS3=@phi-4                COEFFICIENT3=1
# ...
# as follows (Click the red comment above to revert to the short version of the input):
ab_torsionsThe TORSION action with label ab_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details  ATOMS1the four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.  ATOMS2the four atoms involved in the torsional angle=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
ab_refThe CONSTANT action with label ab_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=3.14,3.14,3.14
ab_coeffThe CONSTANT action with label ab_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=2,0.5,1
ab_combThe COMBINE action with label ab_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_comb
vector
the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab_torsions,ab_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab_cosThe CUSTOM action with label ab_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab_comb,ab_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abThe SUM action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=ab_cos 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=ab 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. Notice, also, that in the first two examples the coefficients $c_i$ in the expression above were all set equal to one. In the example above we use the COEFFICIENT keywords to set these quantities to three different values.

Notice, last of all, that in the above examples we reassemble any molecules that have been broken by the periodic boundary conditions using a procedure like that used in WHOLEMOLECULES before calculating the torsion angles. If you wish to turn this off for any reason you use the NOPBC flag as shown below:

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

abThe ALPHABETA action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the alpha beta CV: ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=168,170,172,188 REFERENCEthe reference values for each of the torsional angles=3.14
ATOMS2the atoms involved for each of the torsions you wish to calculate=170,172,188,190 NOPBC ignore the periodic boundary conditions when calculating distances
ATOMS3the atoms involved for each of the torsions you wish to calculate=188,190,192,230
...
# PLUMED interprets the command:
# ab: ALPHABETA ...
# ATOMS1=168,170,172,188 REFERENCE=3.14
# ATOMS2=170,172,188,190 NOPBC
# ATOMS3=188,190,192,230
# ...
# as follows (Click the red comment above to revert to the short version of the input):
ab_torsionsThe TORSION action with label ab_torsions calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_torsions
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details  ATOMS1the four atoms involved in the torsional angle=168,170,172,188 ATOMS2the four atoms involved in the torsional angle=170,172,188,190 ATOMS3the four atoms involved in the torsional angle=188,190,192,230 NOPBC ignore the periodic boundary conditions when calculating distances
ab_refThe CONSTANT action with label ab_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=3.14,3.14,3.14
ab_coeffThe CONSTANT action with label ab_coeff calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_coeff
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1
ab_combThe COMBINE action with label ab_comb calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_comb
vector
the vector obtained by doing an element-wise application of a linear combination to the input vectors: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ab_torsions,ab_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab_cosThe CUSTOM action with label ab_cos calculates the following quantities:
 Quantity   
 Type   
 Description  
ab_cos
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ab_comb,ab_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abThe SUM action with label ab calculates the following quantities:
 Quantity   
 Type   
 Description  
ab
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=ab_cos 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=ab 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

Input

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

Keyword	Type	Description
ATOMS	atoms	the atoms involved for each of the torsions you wish to calculate

Full list of keywords

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

Keyword	Type	Default	Description
ATOMS	input	none	the atoms involved for each of the torsions you wish to calculate
NOPBC	optional	false	ignore the periodic boundary conditions when calculating distances
REFERENCE	optional	not used	the reference values for each of the torsional angles
COEFFICIENT	optional	not used	the coefficient for each of the torsional angles