[gmx-users] g_spatial (gromacs 4.5 manual)

[Atila Petrosian]

Dear gromacs users

I read g_spatial tool of gromacs 4.5 manual. I have many questions.

There are in the manual:

USAGE:
1. Use make ndx to create a group containing the atoms around which
you want the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
4. run g spatial on the xtc output of step #3.
5. Load grid.cube into VMD and view as an isosurface.

In the step 2, [-center tric -ur compact -pbc none] is true or
[-center -ur compact -pbc none]?

In determination of SDF, there are 2 groups:  for example; SDF of the
first (1) group around second (2) group.

In the step 2 of above usage, we should select two groups of the index
file, for centering and for output. How to select these groups? group
1 and then group 2 or group 2 and then group 1? Or there is another
case (all of the system).

In the step 3 of above usage, we should select two groups of the index
file, for least squares fit and for output. How to select these
groups? group 1 and then group 2 or group 2 and then group 1? Or there
is another case (all of the system).

In the step 4 of above usage, we should select two groups of the index
file, to generate SDF and to output cords. How to select these groups?
group 1 and then group 2 or group 2 and then group 1? Or there is
another case.

Please answer my question exactly with determining group numbers in
the each step.

Any help will highly appreciated.

Best regards