[gmx-developers] Extracting i-j forces from nb_generic.c

[James]

Dear Gromacs developers,

To measure thermal conductivity using Green-Kubo I am trying to extract the
i-j atomic forces from nb_generic.c and I wonder if anyone could help me
with some basic questions?

1. If I understand correctly, ii and jj are atom numbers for atom i and
atom j. These don't seem to correspond to the atoms in the order that they
were read in (PDB file), however. How can I recover this order, or what is
the new order?

2. What units are the positions ix, iy, iz (again in nb_generic.c)?

3. nb_generic is within the loop i = i0 to i1-1 in nonbonded.c. What is
this loop? Somehow related to different interaction types?

4. Later, I will also want to extract the instantaneous kinetic and
potential energy of the atom in the same time-step - any advice is very
welcome.

5. Out of interest, I notice many of the files in the release-4-6 branch
are in include/ but the same files are in legacyheaders/ in the master
branch. Why is this? Which should I be developing against?

Any help is greatly appreciated.
Thank you and happy new year!

James
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