This question has been addressed before here on the list.
Well, with rdf at ptraj you get the graphic that shows you the thickness of
the 1st solvation shell.
With this value you feed the watershell command on ptraj (see AmberTools
manual) and then it provides the number of water molecules.
regards,
On Wed, Aug 10, 2011 at 9:46 AM, DEBOSTUTI GHOSHDASTIDAR <
debostutighosh.gmail.com> wrote:
> Hi all
>
> I have a doubt regarding calculating the number of water molecules within
> the first solvation shell of a molecule. Can I do so directly from the
> ptraj
> output of rdf?
> Thanks in advance for your suggestions
>
> --
> Debostuti Ghosh Dastidar
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 10 2011 - 16:30:04 PDT
