[gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

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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