[gmx-users] Re: simulating with air
chaban at univer.kharkov.ua
Wed Aug 13 22:55:35 CEST 2008
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
2008/8/13 Andy Shelley <robert.shelley at gmail.com>:
> 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>
>> 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
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
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