[gmx-users] Regarding calculating the water orientation profile
mark.j.abraham at gmail.com
Thu Nov 23 13:36:12 CET 2017
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 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
> 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,
> Ph.D Student
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