From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Thu Jan 18 2018 - 18:46:46 CST
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
The script I attached is one I found while back for printing x,y,z
coordinates, it might be of some use to you.
On Thu, Jan 18, 2018 at 4:22 PM Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
> 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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