[gmx-users] interaction lists in idef.h

[wnoid at hec.utah.edu]

hello all.



i am trying to trying to write an analysis program that takes advantage
of the gromacs utilities/structures.  for my analysis i need to identify
each type of interaction in the potential energy function and the atoms
involved in each equivalent interaction of the given type.  for example,
for each different type of bond angle, i would like to identify each
triple of bonded atoms forming the given type of bond angle.  also i
would like to be able to identify each pair of atoms - one of type A and
one of type B - that interact through a nonbonded (lennard-jones type)
A-B interaction.



i would like to use something like "read_tps_conf" to read a tpr file
and then extract these lists of pairs, triples, etc. from the
interaction list in the topology data structure.  however, after
spending some time fiddling around with interaction list data structures
such as idef and ilist, it is still not obvious to me how to extract
this information.  after reading through types/idef.h, it seems that the
information i need is stored in these structures, but i still don't
understand how they are used.  is there a relatively easy way to get
these lists of interactions for each interaction type out of the tpr
file?  and if so, can someone please enlighten me as to how this is done?



of course this information can be obtained from the .top file and i have
started writing my own utility for extracting this information directly
from the .top file.  however, if there is a clean way to extract the
information from the .tpr file using gromacs utilities that are already
written, that would be a big help.



thanks to anyone who can help me out here.



will noid