Gencoords

GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric models generates the fundamental building block and arranges multiple copies in a starting configuration, typically along a parametric space curve. The software is designed to allow for easy expansion and user defined arrangements and patterns.

The output consists of three types of files:

• pysites.xyz: Defines a rigid body multi-site building block by specifying the position, orientation and repulsive and attractive interaction strengths of a set of PY sites. The file format is understood by GMIN via use of the PY keyword. The building block can be visualised directly in vmd with the plotGMINMs.tcl script in the SCRIPTS directory of the group software.

• coords: A list of the positions and orientations of N building blocks. There are 3N floats arranged in 3 columns for the xyz positions of the centre of gravity of each building block, followed by 3N floats arranged in 3 columns defining the angle-axis rotation of each building block. This is distinct from the usual coords file definition in which only the positions need to be defined.

• ellipsoid.model.xyz: The data in coords is convolved with the pysites.xyz file to produce a definition of all the PY ellipsoids in the configuration. The format is the same as the pysites.xyz file and can be plotted in VMD using the plotGMINMs.tcl function in the SCRIPTS directory of the group software. This is the same format as the output of the GMIN PY keyword.

The input consists of a single file:

• ellipsoid.model defines the parameters used to drive the creation of the ellipsoid arrangement.

There are at present a number of genCoords Models defined.