[gmx-developers] g_sdf spatial distribution function

Anton Feenstra feenstra at few.vu.nl
Thu Aug 24 09:22:12 CEST 2006

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 the
> gromacs-3.3 release. For a system of 32K atoms and a 50ns trajectory, the SDF
> 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 also
> 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 find
> 3-4 atoms in a widely mobile group like a free amino acid in solution works
> 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 coords
> that are going to be used in the first and subsequent run through trjconv.
> However, be sure to set the -nab option to a sufficiently high value since
> memory is allocated for cube bins based on the initial coords and the -nab
> (Number of Additional Bins) option value.

Put this in 'desc' also:

> 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 selecting
> 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 solute
> that is smaller than the box size. In other circumstances, things might get strange.

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                                     |
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