From: Vermaas, Joshua (
Date: Mon Jan 08 2018 - 11:58:15 CST

Nanotubes are to a first approximation cylindrical. Figure out your radius and height for the cylinder, and something like:

same residue as (x*x+y*y<40*40 and abs(z)<30)

would select your molecules that are within 40 Angstrom of the z axis and within 30 Angstrom of the origin. You've got a ton of options.


On 01/06/2018 06:56 AM, Ashar Malik wrote:
One way would be to use "measure minmax" on a selection having your nanotube.

That will return minmax on x/y/z coordinates of your nanotube.

Then repeat the same process for a selection of your entire system.

That will return minmax on x/y/z coordinates of the whole system.

Now you can select waters between

x-max of tube and x-max of system AND y-max of tube and y-max of system AND z-max of tube and z-max of system OR (the same selection as before with mins).

I think something like this (although it would need a few hit and trys) would do what you want.

To make a selection like this have a look at this:>

This may not be the best way - but it is a way.

On Sun, Jan 7, 2018 at 1:06 AM, Suresh Ghimire <<>> wrote:
Dear vmd user,
I am not being able to remove water outside of carbon nanotube after addition of my water solvation box. How can I remove water molecule outside the tube such that water lies only inside the tube ?. Here I am working on different physical behavior of water inside carbon nanotude : it can be use for water purification.

Tribhuvan University, Patan Multiple Campus
Lalitpur, Nepal