[gmx-users] Regarding calculating the water orientation profile

[Mark Abraham]

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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