From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 07 2007 - 08:54:06 CDT

On Tue, 7 Aug 2007, Christopher Stiles wrote:

hi christopher!

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

very commendable.

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

i suggest you contact bob johnson (in cc), a graduate student in
our group here in philly and our local expert in using VMD for
analysis and visualization of data from simulations of carbon
nanotubes and anything that you would want to put next to them.
over the last couple of years he has done some truely amazing
stuff with VMD for his project.

cheers,
  axel.

CS>
CS>
CS>
CS> Here is the code that I try and put into the "Tk console":
CS>
CS> set NT_beg 1.0
CS>
CS> set NT_end 2.231
CS>
CS> set x_NT 1.6125
CS>
CS> set y_NT 1.6125
CS>
CS> set NT_radius 0.409
CS>
CS> set wat_inside [atomselect 0 "water" and (z > $NT_beg and z < $NT_end and
CS> sqrt((x-$x_NT)*(x-$x_NT) + (y-$y_NT)*(y-$y_NT)) < $NT_radius)]
CS>
CS>
CS>
CS> Thank you,
CS>
CS>
CS>
CS> ~Christopher Stiles
CS>
CS> College of Nanoscale Science and Engineering (CNSE)
CS>
CS> State University of New York, Albany, New York 12203, USA
CS>
CS>
CS>
CS>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.