[gmx-users] Re: simulating with air
robert.shelley at gmail.com
Wed Aug 13 21:51:13 CEST 2008
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.
On Wed, Aug 13, 2008 at 2:14 AM, Vitaly Chaban <chaban at univer.kharkov.ua>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
> 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.
> 2008/8/13 Andy Shelley <robert.shelley at gmail.com>:
> > Vitaly,
> > You mention correct FF for each gas component. I essentially want 78% of
> > 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
> > If not what would be the shortcomings.
> > Thanks,
> > Andy
> > On Fri, Aug 8, 2008 at 8:09 AM, Vitaly Chaban <chaban at univer.kharkov.ua>
> > 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: chaban at univer.kharkov.ua
> >> skype: vvchaban
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