[gmx-developers] coordinates in 'atom in the box' state

[Gaurav Goel]

I'm trying to understand in what "state" the coordinates are stored
during the mdrun.

In chapter 3 of the manual, I read this under "Grid Search"
The grid search is schematically depicted in Fig. 3.5. All particles
are put on the NS grid, with the
smallest spacing >= Rc/2 in each of the directions. In the direction
of each box vector, a particle
i has three images. For each direction the image may be -1,0 or 1,
corresponding to a translation
over -1, 0 or +1 box vector.

I am specifically interested in state of coordinates when they are
given as input to the 'do_update_md'
subroutine to be updated based on current forces (and velocities). Are
they in the state "0", i.e. the atom
in the box state printed out to confout.gro at the end of simulation.

I'm interested in this information because I want to locate particles
in two planar shells centred at z=L/8 and z=3L/8,
where L is the box vector length.

I printed out the coordinates from 'do_update_md' subroutine and all
the values for particle coordinates
are in the range [0,L]. Does that mean those coordinates are already
in the 'atom in the box' state? And,
I can simply use these values to locate particles in two shells.

I will greatly appreciate yo taking time to help me with this.

Thanks,
Gaurav