[gmx-users] Analysis of CNT in water solution

Robert Johnson bobjohnson1981 at gmail.com
Mon Aug 6 17:11:16 CEST 2007

The best and easiest way to do this would be to write a script within
VMD. You can define an atom selection something like:
set wat_inside [atomselect $mol_id "same residue as 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)]

Here $mol_id is the molecule id of your system (probably 0), $NT_beg
and $NT_end are the beginning and ending coordinates (in the
z-direction) of your nanotube, $x_NT and $y_NT are the x and y
coordinates of the nanotube center, and $NT_radius is the nanotube

Then you can loop over the frames in your trajectory and update that
atom selection with the commands:
$wat_inside frame $n
$wat_insde update

Then you can figure out how many water molecules are within your nanotube by
$wat_inside num


On 8/5/07, Christopher Stiles <CS145331 at albany.edu> wrote:
> I am trying to look at the # of water molecules within the CNT as a function
> of time and I was wondering if there was another app like Trjorder that
> maybe instead of using a group of molecules as the reference you could use
> coordinates i.e. the axis of the CNT, or if there is a better way to go
> about this?
> Information on the setup; it is a 2.81700   2.81700   3.35410 box with a ( 6
> , 6 ) CNT (centered in the box) and 811 spc216 molecules and it is at 300k
> and run for 200ps.
> Thank you for help,
> ~Christopher Stiles
> College of Nanoscale Science and Engineering (CNSE)
> State University of New York, Albany, New York 12203, USA
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