From: Giacomo Fiorin (
Date: Fri May 26 2017 - 01:07:00 CDT

Hi Karteek, I have encountered the same problem in CG model development
(with a 3 to 1 mapping instead of MARTINI's 4 to 1, but it's a very similar

Our approach was to not use the RDFs with water, and look at transfer free
energies across interfaces instead.

If you are developing a CG model for water itself, you are going to have to
use other properties than the RDF.


On Thu, May 25, 2017 at 11:35 PM, Peter Freddolino <>

> 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.

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD