[gmx-developers] g_sdf, who developed it?

[Tsjerk Wassenaar]

Hi Chris, David,

Correct me if I'm wrong, but it seems that

g_spatial generates the spatial distribution function of a set of
atoms around another (reference) set of atoms, defining the space by
fitting the reference atoms. g_spatial thus allows constructing an SDF
of water around a protein or micelle.

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.

So they are loots of the same tree, but quite distinct in their application.

Cheers,

Tsjerk

On Thu, Jun 3, 2010 at 8:18 AM,  <chris.neale at utoronto.ca> wrote:
> I wrote g_spatial. I have never used g_sdf, but the programs are not exactly
> identical. Ideally they might be combined, but I looked into that a while
> ago and it is beyond my abilities.
>
> - g_sdf does a fitting based on (I think) 3 atoms defined by the user.
> - g_spatial requires the user to do all of the fitting via trjconv.
>
> In my opinion, it is easier and more robust to require the user to first
> pre-process the trajectory with trjconv. Nevertheless, I see more users on
> the list inquiring about g_sdf; It is impossible to discern if this is
> because g_sdf is harder to use or because it is more often used.
>
> The reasons to use g_spatial, are that one might want to fit based on some
> arbitrary routine, and this should always be possible via trjconv. In my
> opinion, the only thing that favours g_sdf is that one doesn't need to have
> the disk space to store a fit trajectory prior to running g_sdf -- and this
> could be a big plus for g_sdf in some cases.
>
> In the end, I can only comment that I and my colleagues find g_spatial to be
> very useful. Also, from a simple magnitude of the comments on the list,
> there is also a desire to use g_sdf.
>
> Obviously you're close to a release and not wanting to do more coding, but I
> note that the idea behind g_spatial was to keep it simple... let trjconv do
> all of the heavy lifting. Perhaps it would be possible in the future to add
> a new trjconv option to do whatever fitting is done in g_sdf?
>
> Sorry I can't be definitive here,
> Chris.
>
> Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
>
>> On 2010-06-03 06.19, Tsjerk Wassenaar wrote:
>>>
>>> Hi David, Chris,
>>>
>>> The bug referred to concers make_ndx, not g_sdf. I indeed made a few
>>> changes in the code, but those were minor adaptations required to have
>>> it work with GMX3.3.1, such as changing gmx_fatal statements.
>>>
>> oops it should be
>>
>> http://bugzilla.gromacs.org/show_bug.cgi?id=356
>>
>> An additional problem is that we have two seemingly identical programs,
>> g_sdf and g_spatial
>> Chris: did you develop the latter then?
>>
>> Question is whether we need both...
>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>>
>>> On Wed, Jun 2, 2010 at 10:39 PM,<chris.neale at utoronto.ca>  wrote:
>>>>
>>>> g_sdf was developed by Christoph Freudenburger. It was uploaded and
>>>> supported with mailing-list assistance by Dallas Warren:
>>>> http://lists.gromacs.org/pipermail/gmx-users/2005-August/016578.html
>>>>
>>>> Looks like it was also modified by Tsjerk Wassenaar (to work with
>>>> 3.3.1):
>>>>
>>>> http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software
>>>>
>>>> Quoting David van der Spoel<spoel at xray.bmc.uu.se>:
>>>>
>>>>> Hi,
>>>>>
>>>>> I forgot who contributed the code for g_sdf, but there seems to be a
>>>>> strange problem with the code. Maybe he/she with insight in the innards
>>>>> of the program can have a look at
>>>>> http://bugzilla.gromacs.org/show_bug.cgi?id=367
>>>>>
>>>>> Thanks,
>>>>> --
>>>>> 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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>>>>
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>>
>>
>> --
>> 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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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

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