[gmx-users] Analysis of CNT in water solution

[Christopher Stiles]

I have been able to obtain a radial distribution function using "g_rdf -f
traj.xtc -n index.ndx -o -com -xy -b 100" and I have been working with
trjorder to get the 3 of water molecules with in the tube, the best results
so far have been with looking at the center of mass of the CNT, although I
can not expand the radius enough to get the whole inside of the tube with
out including water outside the tube. Is there a way to get this to work as
a cylinder instead of a sphere? Or many put some other reference group in
that will have no effect on the simulation and have a fixed position (i.e.
along the center of the cylinder)?

Thank you for help,

~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE)

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

 

 

  _____  

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Christopher Stiles
Sent: Sunday, August 05, 2007 11:57 PM
To: 'Discussion list for GROMACS users'
Subject: [gmx-users] Analysis of CNT in water solution

 

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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