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 > _______________________________________________ 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
