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 > > >
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