[gmx-developers] Any interest in a g(x, y.z) functionality for g_rdf?

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 11 19:10:35 CET 2011

On 2011-03-11 17.39, Berk Hess wrote:
> Hi,
> Sound interesting, but I don't understand what x, y and z would mean.
> Are those linked to the reference molecule coordinate frame?
> g_densmap does that in 2D, in which case you can still visualize things
> easily. But I can see 3D can be necessary in some cases.
And how does this compare to g_sdf and g_spatial? It would be great if 
these tools were merged into some kind of small library, avoiding the 
overlap in the code and more modular.

Something like this is implemented in g_dipoles as well.
> Berk
> On 03/11/2011 05:22 PM, Shirts, Michael (mrs5pt) wrote:
>> Hi, all-
>> Is there any interest in a g(x,y.z) functionality for g_rdf? For many
>> molecules, the liquid structure can be more complicated, and the
>> ability to
>> visualize it in three dimensions could be useful. We're looking at
>> this in
>> my lab, and were thinking about just writing an easier postprocessing
>> script, but if there is more demand for it, we can implement it in
>> Gromacs
>> as well.
>> Best,
>> ~~~~~~~~~~~~
>> Michael Shirts
>> Assistant Professor
>> Department of Chemical Engineering
>> University of Virginia
>> michael.shirts at virginia.edu
>> (434)-243-1821

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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