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

From: Rabeta Yeasmin (
Date: Fri Jan 19 2018 - 13:13:31 CST

Dear Haddad,

Thanks for your information. I have tried the way you suggest. But the
problem is, it can find out the water which are within the range selected
(lipid bilayer) that means the waters which penetrates the lipid in each
frame. But when I had checked trajectory visually in VMD, I have seen that
there are many waters which penetrates the lipid bilayer but they do not
actually cross through the lipid bilayer rather they come out of the lipid
after a while.
And also the lipid boundary changes from frame to frame. Like, in the first
frame it was from -25 to 31 but after around 3000 frame it become -15 and


Rabeta Yeasmin

On Thu, Jan 18, 2018 at 6:46 PM, Bassam Haddad <> wrote:

> Hi Rabeta,
> While this may not be the quickest approach, I would write a .tcl script
> that does the following:
> 1. iterates through the frames of the simulation and outputs the *resid* of
> any water molecule that penetrates the lipid bilayer, simply by selecting
> ...for example... set lip_wat [atomselect top "water and (z >
> *lower_lipid_boundary* and z < *upper_lipid_boundary*)"] then print the
> *resid*'s of the selection before moving to the next frame.
> 2. after all penetrating water molecules are identified, your script would
> reiterate through the simulation and output the waters' oxygen coordinates
> and time-step. you can then analyse that data to find the velocity of the
> water molecules.
> The script I attached is one I found while back for printing x,y,z
> coordinates, it might be of some use to you.
> ~ Bassam
> On Thu, Jan 18, 2018 at 4:22 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

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