[gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

Hi Joao Sir,
Yes, that was me, who had asked the questions some time ago, but i had no
success in this.



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On Fri, Nov 24, 2017 at 12:11 AM, João Henriques <
joao.m.a.henriques at gmail.com> wrote:

> Wait, now I remember, you even approached me in a private message and we
> exchanged quite a few emails. Did you try any of my suggestions? No
> success?
>
> J
>
> On Thu, Nov 23, 2017 at 7:36 PM, João Henriques <
> joao.m.a.henriques at gmail.com> wrote:
>
> > Hi,
> >
> > I clearly remember replying to something similar sometime ago, and I'm
> > almost sure the post was yours. It may be a good idea to rummage through
> > the mailing list, because I'm pretty sure this type of analysis has been
> > discussed here more than once.
> >
> > Cheers,
> > J
> >
> > On Thu, Nov 23, 2017 at 4:41 PM, 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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> >>
> >>
> >> --
> >> With Best Regards,
> >>
> >> DILIP.H.N
> >> Ph.D Student
> >> --
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student