distance 

corresponds to the
distance
separating two selected atoms:
abf1: index of the
first atom of
the reaction coordinate;
abf2:
index of the
second atom of the reaction coordinate.




distancecom 

corresponds
to the
distance separating the center of mass of two sets of atoms, e.g. the distance
between the
centroid of two benzene molecules:
abf1: list of
indices of atoms
participating to the first center of mass;
abf2:
list of
indices of atoms participating to the second center of mass.




abscissa
new


The
distance between
the centers of mass of two sets of atoms along a given direction. The
word direction
denotes a
vector, i.e.
a Tcl list of
three real numbers, defining the direction of interest:
abf1: list of
indices of atoms
participating to the first center of mass;
abf2:
list of
indices of atoms participating to the second center of mass.
abf3:
list of
indices of atoms forming the system that moves along the vector defined
by abf1 and abf2.




zCoord 

The
distance
separating two groups of atoms along the zdirection of
Cartesian space.
This reaction coordinate is useful for the estimation of transfer free
energies between two distinct media:
abf1: list of
indices of reference
atoms;
abf2:
list of
indices of atoms of interest  e.g.
a solute.




zCoord1atom 

This order
parameter
is similar to zCoord,
but
using a single atom of
interest:
abf1: list of
indices of reference
atoms;
abf2:
index of an
atom of interest




xyDistance 

The
distance
between the centers of mass of two atom groups, projected on the (x, y) plane:
abf1: list of
indices of atoms
participating to the first center of mass;
abf2:
list of
indices of atoms participating to the second center of mass.




gyration
new


The radius
of
gyration of an ensemble of atoms.
abf1: list of
indices of atoms
participating to the computation of the radius of gyration.




dihedral
new


The
dihedral angle
formed by a sequence of four atoms:
abf1: list of indices of the four
atoms defining the torsion.




