[gmx-users] Fwd: Regarding trjorder

[Venkat Reddy]

Dear Sir,

Thanks for the prompt reply. I want to analyse the structural and dynamical
properties of water in the 1st shell of protein. Using the trjorder command
I have obtained the ordered water around the protein within 5A. I would
like to know how I could use the trjorder output pdb to selectively analyze
the radial distribution (RDF) and the mean squared displacement (MSD) of
only the 1st shell water using g_rdf and g_msd.

Thank you


On Mon, Mar 3, 2014 at 2:27 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> I don't know what you are seeking, a definition of the first shell, or of
> "how to analyse."
>
> Mark
> On Mar 3, 2014 6:08 AM, "Venkat Reddy" <venkat4bt at gmail.com> wrote:
>
> > Hello,
> >
> > I have used the trjorder command to order water around 5 Angstrom radius
> of
> > a protein. Can anyone suggest how the obtained pdb file can be used to
> > analyse the system considering only this first shell of water around the
> > protein?
> >
> > Please help me in this regard.
> >
> > Thanks
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> >
> >
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036