[gmx-users] Re: simulating with air

Vitaly Chaban chaban at univer.kharkov.ua
Wed Aug 13 09:14:23 CEST 2008

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 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 <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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