Hi. Though not a GROMACS user, I always read the very interesting topics of the mailing list. In this case I could maybe even help :) There is some info about building nanotubes in the GROMACS wiki/mailinglist and some nice papers about CNTs made with GROMACS by a someone called Johnson (if I remember well). Anyway, I would suggest to keep the nanotube rigid, as long as I suppose you will only simulate a part (in PBC) of a real one and this part can be considered rigid (see also what has been done in the literature). Not much will change if you keep it flexible, and you will spare a lot of computational time. Then, of course, it depends on what you are trying to calculate and if you are operating (as I suppose) in PBC. What I would pay much attention, though, is the VdW potential between the C atoms in the nanotube and your gas molecules, as well as the type of nanotube.
Bye Giulio Message: 2 Date: Sun, 24 Jan 2010 10:46:46 +0330 From: leila karami <karami.lei...@gmail.com> Subject: [gmx-users] gas adsorption on CNT To: gmx-users@gromacs.org Message-ID: <f63182a1001232316k58b42600y29f538d3642b6...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi,I want to simulate gas adsorption on finite CNT. Does CNT be flexible or rigid? which is better? thanks -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php