SIMONAPreprocessor
Possible movements

All moves that Simona can perform are listed and explained here.

The Class documentation can be found Modules

Bond stretching
This move changes the distance $ d_{ij} $ between the atoms i and j.
Bond.png
Angle bends
This move changes the angle between the bond of atoms (i, j) and the bond between the atoms (j, k).
Angle.png
Dihedral move
Allows rotations of the protein's dihedrals.
Dihedral.png
Dihedral angles of the mainchain are called psi ( $ \psi $) or phi ( $ \phi $), angles of sidechains are called chi ( $ \chi $).
If the involved atoms are $ C, N, C_{\alpha}, C$ the angle is a phi-angle: $ \phi_{C N C_{\alpha} C} $
If the involved atoms are $ N, C_{\alpha}, C, N$ the angle is a psi-angle: $ \psi_{N C_{\alpha} C N} $
Rigid body translation
This move translates a whole molecule.
D_RBT.png
Rigid body rotation
This move rotates a whole molecule.
D_RBR.png