Very interesting... At present I work with CNTs as well. Although together with non-aqueous liquids and electrolyte solutions.
Yes, you can use morse terms for gases, just consult the Chapter 5 of the manual how to make your own parameter file (or modify the existing one). 2008/8/13 Andy Shelley <[EMAIL PROTECTED]>: > Vitaly, > > What I am trying to do is simulate a CNT in air and measure temperatures. I > have found a paper that uses Morse potentials for Nitrogen and Oxygen. I am > not familiar with how to use Morse potentials. Can I use morse potentials > for air and Lennard-Jones for the CNT at the same time? If so, any guidance > would be appreciated. > > Thanks, > Andy > > On Wed, Aug 13, 2008 at 2:14 AM, Vitaly Chaban <[EMAIL PROTECTED]> > wrote: >> >> Hi Andy, >> >> To be absolutely correct air contains not only oxygen and nitrogen but >> also other components, so when I mentioned about 'hard work' I meant >> pointing out all the gases (and their fractions) usually present in >> the atmospheric air. >> >> As for FF, I suggest you to find original papers where O2 and N2 >> respectively were simulated and make your own .itp file with these >> parameters. It is always much better to have an ideal source of >> potentials if you're further about to print the results of your >> simulation. >> >> The possible problem of the gromacs force field is that it is not >> constructed for single O2 and N2 molecules and, again, not for the >> gaseous state. However, I think if you use LJ-12-6 parameters they >> would appear close enough both in the gromacs FF and anywhere else. >> >> Pls. let me know if you need further help or guide. >> >> Best, >> Vitaly >> >> >> 2008/8/13 Andy Shelley <[EMAIL PROTECTED]>: >> > Vitaly, >> > >> > You mention correct FF for each gas component. I essentially want 78% of >> > the >> > molecules nitrogen and 22% oxygen. What do you mean by correct FF could >> > I >> > use the encad all atom forcefield to simulate air with correct >> > parameters? >> > If not what would be the shortcomings. >> > >> > Thanks, >> > Andy >> > On Fri, Aug 8, 2008 at 8:09 AM, Vitaly Chaban <[EMAIL PROTECTED]> >> > wrote: >> >> >> >> >I would like to use air as a "solvent" with genbox instead of water. I >> >> > have >> >> >read the manual but have not found any information to help me. Any >> >> >information would be beneficial. >> >> >> >> With air? What is air? A mixture of gases... >> >> >> >> Well, you have to work hard to make such box. Pay attention to make a >> >> proper density... 'genconf' and 'genbox' will appear very useful for >> >> your pursue. >> >> >> >> When you make such box of 'air' and correct FF for each gaseous air >> >> component please upload it to the gromacs site into the 'user >> >> contribution' section. It should be very useful brick for somebody. >> >> >> >> >> >> -- >> >> Vitaly V. Chaban >> >> School of Chemistry >> >> National University of Kharkiv >> >> Svoboda sq., 4, Kharkiv 61077, Ukraine >> >> email: [EMAIL PROTECTED] >> >> skype: vvchaban >> > > > -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
