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

From: Rabeta Yeasmin (
Date: Thu Jan 18 2018 - 18:43:06 CST

Dear Mr. Giacomo,

Thanks for your reply. I have used pbc unwrap to unwrap water. But my
concern is how can I analyse results (may be dcd file) to find out water
molecules passing through the channel.

Rabeta Yeasmin

On Thu, Jan 18, 2018 at 6:38 PM, Giacomo Fiorin <>

> Try using pbc unwrap and analyze the result?
> On Thu, Jan 18, 2018 at 7:19 PM, Rabeta Yeasmin <>
> wrote:
>> 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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