[gmx-users] Regarding calculating the water orientation profile

[João Henriques]

Orientation has nothing to do with proximity. You can have orientation as a
function of proximity, but orientation *per se* does not necessarily
involve a distance, it just tells you about a preferential orientation of
the water molecules towards a reference. We've already been through this in
detail when I suggested looking at the angular probability function,
defining the vectors you want to compute the angle from, etc. I really
don't understand what is hindering you from performing such analysis, which
seems to be exactly what you want/need.

J



On Fri, Nov 24, 2017 at 9:08 AM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> 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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> > > > > --
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> > > DILIP.H.N
> > > Ph.D Student
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>
> DILIP.H.N
> Ph.D Student
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