[gmx-developers] g_sdf, who developed it?

[Mark Abraham]

----- 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
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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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