Action: TORSION

Module	colvar
Description	Usage
Calculate one or multiple torsional angles.
output value	type
the TORSION involving these atoms	scalar/vector

Details and examples

Calculate one or multiple torsional angles.

This command can be used to compute the torsion between four atoms as shown by the input below:

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

tThe TORSION action with label t calculates the following quantities:
 Quantity   
 Type   
 Description  
t
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t FILEthe name of the file on which to output these quantities=COLVAR

Alternatively you can use this action to calculate the angle between two vectors projected on the plane orthogonal to an axis. The example below uses this syntax and computes the cosine of the torsion that was calculated in the first example input above.

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

tThe TORSION action with label t calculates the following quantities:
 Quantity   
 Type   
 Description  
t
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details VECTORAtwo atoms that define a vector=2,1 AXIStwo atoms that define an axis=2,3 VECTORBtwo atoms that define a vector=3,4 COSINE calculate cosine instead of dihedral
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t FILEthe name of the file on which to output these quantities=COLVAR

If you combine this sytax with the functionality in FIXEDATOM you can see how we can calculate the torsional angle between two bond vectors around the z-axis as shown below:

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

a0The FIXEDATOM action with label a0 calculates the following quantities:
 Quantity   
 Type   
 Description  
a0
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,0
a0: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,0  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
azThe FIXEDATOM action with label az calculates the following quantities:
 Quantity   
 Type   
 Description  
az
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,1
az: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,1  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
t1The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Type   
 Description  
t1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details VECTORAtwo atoms that define a vector=1,2 AXIStwo atoms that define an axis=a0,az VECTORBtwo atoms that define a vector=5,6
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t1 FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=20

If you are working with a protein you can specify the special named torsion angles $\phi$, $\psi$, $\omega$ and $\chi_1$ by using TORSION in combination with the MOLINFO command. This can be done by 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 somethingt1The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Type   
 Description  
t1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe 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. 
t2The TORSION action with label t2 calculates the following quantities:
 Quantity   
 Type   
 Description  
t2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t1,t2 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.

If you would like to calculate multiple torsion angles at the same time you can use a command like the one shown below:

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 somethingt1The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Type   
 Description  
t1
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=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.  ATOMS3the four atoms involved in the torsional angle=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information.  ATOMS4the four atoms involved in the torsional angle=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information.  ATOMS5the four atoms involved in the torsional angle=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t1 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

This input tells PLUMED to calculate the $\phi$ angles in residues 3-7 of the protein. The output, t1, is a 5 dimensional vector.

Notice that you can also use the VECTORA, VECTORB axis syntax when calculating multiple torsions as shown below:

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

tThe TORSION action with label t calculates the following quantities:
 Quantity   
 Type   
 Description  
t
vector
the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details ...
  VECTORA1two atoms that define a vector=2,1 AXIS1two atoms that define an axis=2,3 VECTORB1two atoms that define a vector=3,4
  VECTORA2two atoms that define a vector=6,5 AXIS2two atoms that define an axis=6,7 VECTORB2two atoms that define a vector=7,8
  VECTORA3two atoms that define a vector=10,9 AXIS3two atoms that define an axis=10,11 VECTORB3two atoms that define a vector=11,12
...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=20

This input would output a three dimensional vector of torsion angles.

The last thing to note is that by default a procedure akin to that used in WHOLEMOLECULES is used to ensure that the sets of atoms that are specified to each ATOMS keyword or set of VECTORA, AXIS and VECTORB keywords are not broken by the periodic boundary conditions. If you would like to turn this off for any reason you add the NOPBC in your input file as shown below:

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

tThe TORSION action with label t calculates the following quantities:
 Quantity   
 Type   
 Description  
t
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4 NOPBC ignore the periodic boundary conditions when calculating distances
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t FILEthe name of the file on which to output these quantities=COLVAR

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 four atoms involved in the torsional angle
AXIS	atoms	two atoms that define an axis
VECTORA	atoms	two atoms that define a vector
VECTORB	atoms	two atoms that define a vector

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 four atoms involved in the torsional angle
AXIS	input	none	two atoms that define an axis
VECTORA	input	none	two atoms that define a vector
VECTORB	input	none	two atoms that define a vector
NOPBC	optional	false	ignore the periodic boundary conditions when calculating distances
COSINE	optional	false	calculate cosine instead of dihedral

deprecated keywords

The keywords in the following table can still be used with this action but have been deprecated

Keyword	Description
VECTOR1	You should use VECTORA instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only
VECTOR2	You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only