From: Peter Freddolino (
Date: Thu May 25 2017 - 22:35:38 CDT

Well in that case, the tricky part is in deciding how to cluster the all
atom waters into CG waters. If you are doing a 4->1 mapping, how do you
choose which AA waters to turn into a single CG water? How do you decide
what is the optimal mapping? This is a non-trivial problem that CG
builder circumvents by just trusting the atom numbering. For your
application you're going to need to come up with your own rules for the
mapping, and recognize that your results may be highly dependent on
which waters you cluster into beads.

On 05/25/2017 11:31 PM, Karteek Kumar wrote:
> If I understood your mail correctly, the solution is more towards
> creating the configuration for the CG models.
> Actually, I am trying to get the RDF from the mapped CG trajectory of
> AA water box.
> We have developed CG potentials and want to compare the CG structure
> with AA mapped trajectory.