Ellipsoid.xyz

The ellipsoid.xyz file is the output of GMIN when using the PY keyword.

The file defines the positions and orientations of the set of repulsive ellipsoids for each PY site defined in the minimisation.

The format of the file is:

n

comment

A1 x1 y1 z1 ellipse ra1 rb1 rc1 m111 m121 m131 m211 m221 m231 m311 m321 m331 atom_vector p11 p21 p31

A2 x2 y2 z2 ellipse ra2 rb2 rc2 m112 m122 m132 m212 m222 m232 m312 m322 m332 atom_vector p12 p22 p32

...

An xn yn zn ellipse ran rbn rcn m11n m12n m13n m21n m22n m23n m31n m32n m33n atom_vector p1n p2n p3n

The format is based on the standard xyz file format in which the number of sites is specified is the first line (n). The second line is a comment or description. Each of the sites consists of the same pattern of parameters which are defined here:

• Ai: a single char describing the type of the site. This is useful for plotting ellipsoids in different colours.
• xi,yi,zi: floats defining the position of the centre of each ellipsoid.
• rai, rbi, rci: define the length of the axes of the ellipsoid that represents the repulsive interaction of the PY potential.
• m11n m12n m13n m21n m22n m23n m31n m32n m33n: the rotation matrix used to orient each ellipsoid.
• P1i, P2i, P3i: Angle axis orientation of the ellipsoid which should correspond to the rotation matrix.

To plot ellipsoid.xyz files in vmd you can use the plotGMINms.tcl script found in /svn/SCRIPTS/visuals of the group repository. Instructions for doing that are included on the plotGMINms.tcl page.