[gmx-developers] g_sdf, who developed it?

[Tsjerk Wassenaar]

Hi,

On Thu, Jun 3, 2010 at 9:52 AM,  <chris.neale at utoronto.ca> wrote:
> In general, I think that it would be a shame to lose any tool. If there is
> desire to depreciate it due to a difficult-to-isolate bug, then perhaps it
> would be a good general principle to add a warning requiring -maxwarn 1 to
> generate any output. More detailed reply follows.

I concur, albeit that one may need to distinguish and now and then
reconsider classification of tools that deserve active upkeep and
those that are to be stored in an attic for someone to blow the dust
off if deemed useful.

> Basically yes. g_spatial generates a 3D map of a user-defined set of atoms
> as they exist in the input .xtc file. It is up to the user to pre-process
> the .xtc such that, for example, the reference set is fit. It is entirely
> possible to then generate an SDF of the reference set, and separately the
> water, and separately the ions, etc.

Yeah, that was exactly what my notion was.

>> g_sdf generates the spatial distribution function of a set of atoms in
>> the coordinate system defined by another set of atoms, consisting of
>> 1, 2 or 3 atoms, where the final SDF is obtained by averaging over all
>> local coordinate systems thus defined. g_sdf thus allows constructing
>> an SDF of, e.g., water around methanol in a water/methanol mixture.
>
> not sure. Do you mean that g_sdf can average over many particles (e.g. many
> methanol's) in the way that an rdf does? If this is the case, then surely
> g_sdf has some very important features that one does not want to lose.

Exactly.

> I think that this it probably the case. If indeed there is some bug in
> g_sdf, then it probably should be fixed in the long term, and possibly just
> add a warning to the usage for this release.

I was thinking of adding a note also in the description that a bug is
currently open.

> If there is no bug in g_sdf, then I see no problem in keeping two similar
> tools... unless that's creating headaches for the developers. In that case,
> I have no ability to comment.

Well, probably they could merged, or g_sdf could be merged with g_rdf.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands