[gmx-users] water channel

Yao Yao yao0o at ymail.com
Wed Feb 15 03:38:32 CET 2012

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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