VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sat May 13 2017 - 21:36:21 CDT

Hi Karteek,
The problem is that each of your waters is set as a different segment.
CGBuilder won't combine atoms from different segments to form a bead. If
you give all the waters the same segment and chain names, you will get
the expected output.
Best,
Peter

On 05/12/2017 05:48 PM, Karteek Kumar wrote:
> Hi,
>
> Please find the attached pdb and psf files.
>
> Thanks,
> Karteek
>
> On Fri, May 12, 2017 at 4:33 PM, Peter Freddolino <petefred_at_umich.edu
> <mailto:petefred_at_umich.edu>> wrote:
>
> 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
> ###########
>
>
>