distance |
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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.
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distance-com |
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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.
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abscissa
new
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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.
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zCoord |
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The
distance
separating two groups of atoms along the z-direction 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.
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zCoord-1atom |
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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
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xyDistance |
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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.
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gyration
new
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The radius
of
gyration of an ensemble of atoms.
abf1: list of
indices of atoms
participating to the computation of the radius of gyration.
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dihedral
new
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The
dihedral angle
formed by a sequence of four atoms:
abf1: list of indices of the four
atoms defining the torsion.
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