[gmx-users] Regarding calculating the water orientation profile
Dilip H N
cy16f01.dilip at nitk.edu.in
Thu Nov 23 16:49:53 CET 2017
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
And hence it can shed some light on the Hydrogen bond
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On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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?
> 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
> > 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
> > 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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