You can look at gromacs tool g_flux and g_count at:
https://github.com/orbeckst/g_count
Jianguo
________________________________
From: Yao Yao <[email protected]>
To: "[email protected]" <[email protected]>
Sent: Wednesday, 15 February 2012, 10:38
Subject: [gmx-users] water channel
Hi Gmxers,
Happy Valentine's Day!
Sorry, I am still simulating a protein that has water channel.
I was just wondering if there is a way to calculate the water density in the
channel throughout my trajectory.
I was lucky enough to run a NPT simulation. So I guess I can use g_energy to
directly get density.
But since the number of the channel water is quite dynamic, I do not think I
can separate energy group for them in my mdp.
Could someone help me with this?
Thanks,
Yao
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