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 radius. 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 Bob On 8/5/07, Christopher Stiles <[EMAIL PROTECTED]> 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 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
