[gmx-users] g_sdf -> and g_spatial

[Justin A. Lemkul]

Dallas Warren wrote:
> I know, bit of a zombie topic (May 2011) to be digging out of the archives
> here.
> 
> I have previously used g_sdf rather extensively and needed to generate some
> spatial distribution functions for a paper.  Started to looked into g_spatial
> to see if that can do what I want it to, since g_sdf has been removed from
> the distribution.  g_spatial is not what I expected and seems to me to be
> actually less flexible than g_sdf was, though I are more than likely wanting
> to use it slightly differently way to the person that wrote/developed it.
> g_spatial requires a single solute molecule that is relatively stationary and
> centered for the length of the trajectory (which needs some running through
> trjconv to get this done), then it calculates the SDF relative to this
> molecule.  g_sdf makes no such assumption and you can have many molecules
> which you can then calculate and get the average SDF.
> 
> Is there the possibility that we can either have g_sdf added back into the
> distribution (or is there documentation / discussion somewhere that I can
> read to see why it was removed), or the functionality that has been lost
> added into g_spatial (probably not trivial)?  Don't like my chances though
> ;-), but can't hurt to ask.
> 
> I am currently using a 4.0.7 installation of GROMACS, which includes g_sdf,
> to generate the appropriate images I need.
> 

I think the biggest issue with g_sdf was maintenance.  See the discussion here:

http://redmine.gromacs.org/issues/356

The bug discussed is likely still present, as I think the resolution was "get 
rid of the tool."  You can, however, access gmx_sdf.c in src/contrib (at least, 
this is true in the latest release-4-6 from git).  It may constitute a "use at 
your own peril" situation though, if it is (and always has been) buggy.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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