From: Jadzia Dax (
Date: Sat Jan 06 2018 - 06:52:54 CST

​Dear Suresh,

I'm not sure if there is a more elegant way, but I would try it with the
powerful atomselection language of VMD, in particular the two keywords
"within" and "same ... as"​. You could for instance select af few water
atoms in the center of the tube and select all water molecules (using same
residue as) within a certain radius. This might not perfectly work for
every single water molecule, in particular at the ends of the tube, but
these few molecules can then be selected/removed manually. After the
desired atoms are selected you can for instance save them in a new PDB file
with writepdb.

Here are some related links from the user guide which might be useful:


Hope this is helpful.

Best wishes,

On Sat, Jan 6, 2018 at 1:06 PM, 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.
> --
> Student/Researcher
> Tribhuvan University, Patan Multiple Campus
> Lalitpur, Nepal