[gmx-users] Fwd: Regarding trjorder

[Mark Abraham]

On Mon, Mar 3, 2014 at 12:23 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> 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)


This probably neither needs nor wants any ordering or a subset. I would
construct the whole function, and then choose to ignore things past the
first shell, once the rdf shows where the "first shell" ends.


> and the mean squared displacement (MSD) of
> only the 1st shell water using g_rdf and g_msd.
>

Having identified a decent criterion in the first stage, use g_msd with an
index group that matches it (e.g. constructed with g_select). MSD generally
uses a unique reference, so you still don't need to do ordering.

Mark


>
> 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
> --
> Gromacs Users mailing list
>
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> posting!
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