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

From: Giacomo Fiorin (
Date: Thu Jan 18 2018 - 18:38:33 CST

Try using pbc unwrap and analyze the result?

On Thu, Jan 18, 2018 at 7:19 PM, Rabeta Yeasmin <>

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

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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