From: Christopher Stiles (
Date: Tue Aug 07 2007 - 08:41:31 CDT

Just off the bat I am very new to VMD and have went through some of the
tutorials and read the manual to the extent that it deals with Analysis.

I have used Gromacs to simulate a Carbon Nanotube (CNT) in water for a
length of time. I am trying to use VMD to look at the tube and count the
number of water molecules in the tube with respect to time. I have the
following code but I am not sure that I am writing it correct or even going
about it correctly, so any advice would be greatly appreciated!


Here is the code that I try and put into the "Tk console":

set NT_beg 1.0

set NT_end 2.231

set x_NT 1.6125

set y_NT 1.6125

set NT_radius 0.409

set wat_inside [atomselect 0 "water" and (z > $NT_beg and z < $NT_end and
sqrt((x-$x_NT)*(x-$x_NT) + (y-$y_NT)*(y-$y_NT)) < $NT_radius)]


Thank you,


~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE)

State University of New York, Albany, New York 12203, USA