Adk44: Created page with "GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric mode..."

2019-05-13T11:13:25Z

Created page with "GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric mode..."

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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.

Gencoords - Revision history

Adk44: Created page with "GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric mode..."