## g(r) GUI Plugin, Version 1.3

This plugin provides a simple graphical user interface to the `measure gofr`
and `measure rdf` commands in VMD, which calculate the spherical atomic radial
distribution function
*g(r)* between the atom coordinates in two selections over a given trajectory
or a subset thereof. You have to have a trajectory already loaded into VMD and have
the option to either view the resulting *g(r)* and/or the corresponding number
integral in MultiPlot
windows or write the result of the calculation to a file.

### Remarks:

- Selections **have** to be defined (default is empty). Typical radial distribution
functions are computed between elements (same or different), but due to the power of
VMD's selection language syntax, very sophisticated distribution functions may be computed.

- The normalization of *g(r)* has little meaning unless you enable processing of the
periodic boundary conditions and have a fixed set of atoms in the selection. The number
integrals are computed directly and thus provide accurate coordination numbers.

- You can use the 'Set unit cell dimension' dialog from the 'Utilities' menu to set the simulation cell information for all frames of the current molecule.

- The output file created by the save option contains three columns, the value of *r*,
*g(r)*, and the number integral over *g(r)*.

- In case a selection is empty in a frame, an empty histogram is added to the sum over all frames.

- **Optimizations:**

- Do not activate
`Update Selections`unless needed. - If you have CUDA capable hardware, you can try enabling the GPU version. Particularly on large problems, it can be significantly faster, however, it has not been as rigorously tested as thoroughly as the (default) multi-threaded CPU version.
- If you want to look at a 'local' distribution function, i.e. Selection 1 is one atom or
a small number of atoms in close proximity, you should consider using a selection with the
keywords "<
*selection text 2*> and (within <*max r*> of <*selection text 1*>)" or "<*selection text 2*> and (pbwithin <*max r*> of <*selection text 1*>)". This can reduce the execution time**drastically**at the expense of no longer getting a consistent normalization. Since this is usally a qualitative measurement anyways, this should not matter in most cases.

### Literature on *g(r)* calculations.

A short introduction on radial distribution functions can be found at http://en.wikipedia.org/wiki/Radial_distribution_function.

The GPU accelerated CUDA implementation is described in this paper:
B.G. Levine, J.E. Stone and A. Kohlmeyer,
"Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units - Radial Distribution Function Histogramming", J. Comp. Phys, *in Press*, (2011) (http://dx.doi.org/10.1016/j.jcp.2011.01.048)

- J. P. Hansen and I. R. McDonald, Theory of Simple Liquids, Academic Press, London (1986)
- Donald A. McQuarrie, Satistical Mechanics, University Science Books, 2nd Rev Ed edition (2000)
- David Chandler, Introduction to Modern Statistical Mechanics, Oxford University Press, USA (1987)