[gmx-developers] g_sdf, who developed it?

[chris.neale at utoronto.ca]

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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