Thank you very much as always you're a great help BOB! I have about 4 hours till my next simulation finishes so I will let you know how it works then.
~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA >-----Original Message----- >From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] >On Behalf Of Robert Johnson >Sent: Monday, August 06, 2007 11:11 AM >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] Analysis of CNT in water solution > >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 _______________________________________________ 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
