TORSION

This is part of the colvar module

Calculate a torsional angle.

This command can be used to compute the torsion between four atoms or alternatively to calculate the angle between two vectors projected on the plane orthogonal to an axis.

The atoms involved can be specified using

ATOMS

the four atoms involved in the torsional angle

Or alternatively by using

AXIS	two atoms that define an axis. You can use this to find the angle in the plane perpendicular to the axis between the vectors specified using the VECTOR1 and VECTOR2 keywords.
VECTOR1	two atoms that define a vector. You can use this in combination with VECTOR2 and AXIS
VECTOR2	two atoms that define a vector. You can use this in combination with VECTOR1 and AXIS

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
COSINE	( default=off ) calculate cosine instead of dihedral

Examples

This input tells plumed to print the torsional angle between atoms 1, 2, 3 and 4 on file COLVAR.

t: TORSION ATOMS=1,2,3,4
# this is an alternative, equivalent, definition:
# t: TORSION VECTOR1=2,1 AXIS=2,3 VECTOR2=3,4
PRINT ARG=t FILE=COLVAR

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.

MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
t1: TORSION ATOMS=@phi-3
t2: TORSION ATOMS=@psi-4
PRINT ARG=t1,t2 FILE=colvar STRIDE=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 4th residue of the protein.