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 source code can be found in the svn/UTILS/genPySites directory and can be compiled with the command:

pgf90 genCoords.f90 -o genCoords

or variations thereof.

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. See the GMIN documentation for instructions on the PY potential and the format of the pysites.xyz file. To visualise the building block in vmd first convert the file to an ellipsoid.xyz file using pysitesToXYZ.py in the genPySites directory and then plot it using 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 data 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.