Current CVs implemented include:
(i) DISTANCE : distance between two atoms
(ii) COM_DISTANCE: distance between center of mass of two atom groups
(iii) DF_COM_DISTANCE: difference of distances between center of mass of first two atom
groups and second two atom groups
(iv) LCOD: linear combination of distances between pairs of atoms
(v) ANGLE: angle between lines joining atoms
(vi) COM_ANGLE: angle formed by center of mass of three atom groups
(vii) TORSION: dihedral angles
(viii) COM_TORSION: dihedral angle formed by the center of mass of four atom groups
(ix) COS_OF_DIHEDRAL: sum of cosines of dihedral angles
(x) SIN_OF_DIHEDRAL: sum of sines of dihedral angles
(xi) PAIR_DIHEDRAL: sum of cosines of a list of angles
(xii) PATTERN_DIHEDRAL: a pattern-recognizing function defined on a list of dihedral angles
(xiii) R_OF_GYRATION: radius of gyration of a group of atoms
(xiv) MULTI_RMSD: RMS or RMSDs of several groups of atoms with respect to a reference position
(xv) N_OF_BONDS: cv for hydrogen-bonds
(xvi) HANDEDNESS: for handedness of different helices
(xvii) N_OF_STRUCTURES: this counts the number of structures that stay close in the
sense with respect to a group of reference structures
For more details on these CVs, please see the AMBER16 manual.
We are continuously adding new CVs to this list. To incorporate a newly defined and tested
CV for use with ABMD and other modules, please contact sagui@ncsu.edu and/or fpan3@ncsu.edu.
During the coming year, we aim to release a set of quaternion-based CVs for large-scale motions
of a large number of atoms.