[gmx-users] Regarding water orientation profile

[Dilip H N]

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,

DILIP.H.N
Ph.D Student



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