[gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

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