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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 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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