[gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

So what exactly does this Orientation Profile means.??
I am really confused with the exact approach towards it...


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On Fri, Nov 24, 2017 at 12:47 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> "Coming closer" implies you care about distance, but your original question
> was about orientation. So it's unclear what you want.
>
> Mark
>
> On Thu, 23 Nov 2017 16:50 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
>
> > I want to calculate whether the water molecules are coming closer towards
> > the N-terminal or towards the C-terminal of the amino-acid throughout
> the
> > simualtion.
> > And hence it can shed some light on the Hydrogen bond
> > dynamics....hopefully...
> >
> > Thank you
> >
> >
> >
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> >
> > On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > It sounds like to need to be more clear about what you want to
> calculate
> > > before you can sensibly find a tool to do it. You should be able to
> write
> > > down the equation for what you want to compute as your observation long
> > > before you run a simulation, or how will you know what data to collect?
> > >
> > > Mark
> > >
> > > On Thu, 23 Nov 2017 07:26 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
> > >
> > > > Hello Sir,
> > > > I have run a simulation of amino-acid (glycine) with water molecules
> > for
> > > 10
> > > > ns. Now i need to find out/analyze that whether the water molecules
> are
> > > > getting/more oriented towards N-terminal of glycine or towards the
> > > > C-terminal of glycine. (i hope this is what water orientation profile
> > > means
> > > > ie., the preferential orientation of water towards particular
> > > > moeity/group...).
> > > > So, which is the exact module/command to find this..?? wether gmx
> > sorient
> > > > or gmx gangle or gmx angle ..??
> > > >
> > > > How to resolve this issue...
> > > >
> > > > Thank you
> > > >
> > > >
> > > > --
> > > > With Best Regards,
> > > >
> > > > DILIP.H.N
> > > > Ph.D Student
> > > >
> > > >
> > > >
> > > > ‌
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> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student