From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri May 12 2017 - 15:33:54 CDT

You would need to also send your pdb/pdf input files for us to figure
out what could be wrong. My guess is that your waters don't have
consecutive residue numbers...
Best,
Peter

On 05/12/2017 11:37 AM, Karteek Kumar wrote:
> Hello users,
>
> I am trying to obtain the RDF for the mapped All-Atom trajectory for
> martini CG model.
> I have loaded 1000 AA water molecules and used (Extensions -> modeling
> -> CG builder) to create the mapped trajectory.
> I could see 1000 beads but as Martini water CG model is 4:1, I would
> rather expect only 250 beads.
> Even the water.cgc shows that 4 water molecules are grouped.
>
> I am not understanding what I am missing? Any help on this is greatly
> appreciated.
> Alternatively, I would be happy to know any other methods to get RDF
> for the mapped AA trajectory.
>
> Thanks in advance.
> Karteek
>
>
> water.cgc file shows
> #########
> CGBEGIN
> TIP3 H2O 0
> TIP3 OH2 0
> TIP3 H1 0
> TIP3 H2 0
> TIP3 OH2 1
> TIP3 H1 1
> TIP3 H2 1
> TIP3 OH2 2
> TIP3 H1 2
> TIP3 H2 2
> TIP3 OH2 3
> TIP3 H1 3
> TIP3 H2 3
> CGEND
> ###########
>