[gmx-developers] g_sdf spatial distribution function
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Thu Aug 24 21:44:25 CEST 2006
I like the comments provided by Anton. Also, I am happy to merge this with
g_rdf. The effort would be small if the user was still required to do their own
two runs through trjconv first, but I think that this is not desirable for a
general distribution program. 2 questions and a bug post:
1. A proper sdf-capable version of g_rdf would be able to do the fitting and
centering on the fly. I took a look at trjconv and must say that I don't
entirely understand how it's done. Anyone want to give any pointers?
2. When I try trjconv -fit rot+trans -center rect -pbc whole, I don't get the
same results as when I do A(-fit rot+trans)-->B then B(-center rect -pbc
whole)-->C. Anyone know why that is? And more importantly, can I do them in one
step for sdf purposes within g_rdf? I have seen posts that there was an
sdf-capable program at one time, but my emails to the author bounced back to me.
Anyone have a version of that program that I can use to get an idea how to do
BUG: line 216 of 298 should have divided Y and Z by "bohr", not just X as was
previously posted. The correct line is:
Quoting Anton Feenstra <feenstra at few.vu.nl>:
> Hi chris,
> Looks great (the idea, haven't tried your code).
> Some suggestions:
> Put parts of this in *desc:
> > Here is the source code for g_sdf.c that I developed from template.c of
> > gromacs-3.3 release. For a system of 32K atoms and a 50ns trajectory, the
> > can be generated in about 30 minutes, with most of the time dedicated to
> the two
> > runs through trjconv that are required to center everything properly. This
> > takes a whole bunch of space (3 copies of the xtc file). Still, the
> pictures are
> > pretty and very informative when the fitted selection is properly made. I
> > 3-4 atoms in a widely mobile group like a free amino acid in solution
> > well, or select the protein backbone in a stable folded structure to get
> the SDF
> > of solvent and look at the time-averaged solvation shell.
> Put parts of this in *bugs (check which name is used in other
> programs, and pass it to pass_common_args):
> > To reduce the amount of space and time required, you can output only the
> > that are going to be used in the first and subsequent run through
> > However, be sure to set the -nab option to a sufficiently high value
> > memory is allocated for cube bins based on the initial coords and the
> > (Number of Additional Bins) option value.
> Put this in 'desc' also:
> > USAGE:
> > 1. Use make_ndx to create a group containing the atoms around which you
> want the SDF
> > 2. Use trjconv -fit rot+trans selecting the new group for fitting
> > 3. Use trjconv -center rect -pbc whole on the output xtc of step #2
> > the new group for centering.
> > 4. run g_sdf on the xtc output of step #3.
> > 5. Load grid.cube into VMD and view as an isosurface.
> And this also in 'bugs':
> > * This g_sdf was designed for use with a portion of a protein or other
> > that is smaller than the box size. In other circumstances, things might get
> That way, the useful information is present for anyone who might want to
> use your program.
> BTW, I agree with Erik Marklund's comment that this would conceptually
> fit in with g_rdf. I'm not sure if the effort of merging would be worth
> it, though.
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
> | | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
> | | "If You See Me Getting High, Knock Me Down" (RHCP) |
> gmx-developers mailing list
> gmx-developers at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
More information about the gromacs.org_gmx-developers