Ways to find water molecules passing through the water channel in lipid bilayer

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Thu Jan 18 2018 - 18:19:29 CST

Dear NAMD users,

I want to calculate water molecules that are crossing through the channel
of a lipid bilayer. It is very difficult to track water molecules visually
which are passing through the channel in VMD as there are a lot of water
molecules. And also I am confused about the unwrapping the water molecules
to calculate the velocity at which water is passing through the channel.
Because I can track an water molecule passing through the channel visually
but when I check the pdb file, some of its x, y coordinate are outer side
of the simulation box (in unwrapped water molecule). So I wonder if they
are outer side of the simulation box how they cross the channel through the

I will be grateful if anyone can suggest me any way to calculate water
molecules passing through lipid bilayer and their velocity/diffusion rate.


Rabeta Yeasmin

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