[gmx-users] Fwd: Gmx gangle
rose.rhmn93 at gmail.com
Wed Sep 12 10:08:45 CEST 2018
---------- Forwarded message ---------
From: rose rahmani <rose.rhmn93 at gmail.com>
Date: Sun, 9 Sep 2018, 14:45
Subject: Gmx gangle
To: <gmx-users at gromacs.org>
I want to calculate angle between water molecules and ZnS surface(slab). I
mean the angular distribution function(ADF) of ALPHA and BETA. I define to
angles; Alpha= angle between OH bond of water and surface(plane) Beta=
angle between HOH plane and surface(plane).
I used gmax gangle for Alpha:
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
Then i selected water(SOL) group
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
And again i selected water group.
But results are little odd and histograms are two plot which are symmetric
I think sth is wrong. Should i make an index file for OH bond in the case
of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
calculated the angle between COM of water vector and surface not the OH
bond of water. As you know water has 2 OH bond. So... what should i do?
How about BETA? does it really calculate what i want?
Should i make an special index file?
If i want to calculate this property (ADF) in for example 1 nm from
surface, what should i do?
To be more clear, I refer you to fig.1 and fig.8
Would you please help me how can i reach these goals?
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