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
--
========================================
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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