[gmx-users] Regarding water orientation profile

João Henriques joao.m.a.henriques at gmail.com
Tue Oct 31 09:37:47 CET 2017


I've had similar issues in the past with the calculation of angular
distribution functions of water in respect to a given point or amino acid
residue and it wasn't easy/possible to solve with standard gromacs tools.
I'd suggest using MDAnalysis or some other equivalent tool. It definitely
gives you more freedom at the cost of having to code it yourself, plus it
can potentially be slow unless your Python skills are up to the challenge.
Here are a few examples you can use for "inspiration":


In any case, this is probably the least painful solution, since others
would revolve around wrapping one or more gromacs tools with some nasty
scripts, or coding a proper tool in C++ either from scratch or by building
on top of functions already available in gromacs source code.

Hope this helps,

On Tue, Oct 31, 2017 at 8:55 AM, Dilip H N <cy16f01.dilip at nitk.edu.in>

> Hello,
> I want to do the water orientation profile for the amino-acid which is
> surrounded by water molecules as in my case amino-acid+water mixture.
> ie., i want to find out whether the water is orientation is more towards
> the N-terminal or towards the C-terminal of the amino acid and hence the
> orientation profile. I want to know throught the simulation around which
> terminal water molecules are more oriented as a function of time or etc.,
> I have a simulation done in GROMACS with one amino-acid in presence
> of cosolvents which is solvated with water for 10 ns. So I want to have the
> water orientation profile.But i tried with gmx sorient command, but i am
> unable to understand it.. and also through gmx h2order which
> calculates the orientation
> of water molecules with respect to the normal of the box, but i need to
> calculate with respect to N-terminal or through C-terminal.
> What is the best way to solve this..??
> Any suggestions are highly appreciated.
> --
> With Best Regards,
> Ph.D Student
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