[gmx-users] water channel

Jianguo Li ljggmx at yahoo.com.sg
Wed Feb 15 03:54:48 CET 2012

You can look at gromacs tool g_flux and g_count at: 



 From: Yao Yao <yao0o at ymail.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org> 
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?



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