[gmx-developers] g_sdf, who developed it?

[Erik Marklund]

That's good news! I have been thinking about that option before in other 
contexts, passing output form one gromacs tool diretcly into another. 
Great to hear that someone tried it and that it works.

Cheers,

Erik Marklund

Mark Abraham skrev:
>
>
> ----- Original Message -----
> From: chris.neale at utoronto.ca
> Date: Thursday, June 3, 2010 16:19
> Subject: Re: [gmx-developers] g_sdf, who developed it?
> To: gmx-developers at gromacs.org
>
> > 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.
>
> A solution that does not require the existence of excess disk is that 
> of named pipes (http://en.wikipedia.org/wiki/Named_pipe). I've used 
> such in the past to pipe the .xvg output of some GROMACS tool straight 
> to g_analyze, for example. It's straightforward to write a shell 
> script that makes the named pipe, sets up the consumer process in the 
> background and then runs the producer process.
>
> I know nothing about either g_sdf or g_spatial, but perhaps the 
> existence of this technique indicates a consolidation of these tools 
> along the lines suggested by Chris.
>
> Mark
>
> > 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
> > >>>>--
> > >>>>gmx-developers mailing list
> > >>>>gmx-developers at gromacs.org
> > >>>>http://lists.gromacs.org/mailman/listinfo/gmx-developers
> > >>>>Please don't post (un)subscribe requests to the list. Use
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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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-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/