<div dir="ltr">Vitaly,<br><br>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.<br>
<br>Thanks,<br>Andy<br>
<br><div class="gmail_quote">On Wed, Aug 13, 2008 at 2:14 AM, Vitaly Chaban <span dir="ltr"><<a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Andy,<br>
<br>
To be absolutely correct air contains not only oxygen and nitrogen but<br>
also other components, so when I mentioned about 'hard work' I meant<br>
pointing out all the gases (and their fractions) usually present in<br>
the atmospheric air.<br>
<br>
As for FF, I suggest you to find original papers where O2 and N2<br>
respectively were simulated and make your own .itp file with these<br>
parameters. It is always much better to have an ideal source of<br>
potentials if you're further about to print the results of your<br>
simulation.<br>
<br>
The possible problem of the gromacs force field is that it is not<br>
constructed for single O2 and N2 molecules and, again, not for the<br>
gaseous state. However, I think if you use LJ-12-6 parameters they<br>
would appear close enough both in the gromacs FF and anywhere else.<br>
<br>
Pls. let me know if you need further help or guide.<br>
<br>
Best,<br>
Vitaly<br>
<br>
<br>
2008/8/13 Andy Shelley <<a href="mailto:robert.shelley@gmail.com" target="_blank">robert.shelley@gmail.com</a>>:<br>
<div><div></div><div>> Vitaly,<br>
><br>
> You mention correct FF for each gas component. I essentially want 78% of the<br>
> molecules nitrogen and 22% oxygen. What do you mean by correct FF could I<br>
> use the encad all atom forcefield to simulate air with correct parameters?<br>
> If not what would be the shortcomings.<br>
><br>
> Thanks,<br>
> Andy<br>
> On Fri, Aug 8, 2008 at 8:09 AM, Vitaly Chaban <<a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a>><br>
> wrote:<br>
>><br>
>> >I would like to use air as a "solvent" with genbox instead of water. I<br>
>> > have<br>
>> >read the manual but have not found any information to help me. Any<br>
>> >information would be beneficial.<br>
>><br>
>> With air? What is air? A mixture of gases...<br>
>><br>
>> Well, you have to work hard to make such box. Pay attention to make a<br>
>> proper density... 'genconf' and 'genbox' will appear very useful for<br>
>> your pursue.<br>
>><br>
>> When you make such box of 'air' and correct FF for each gaseous air<br>
>> component please upload it to the gromacs site into the 'user<br>
>> contribution' section. It should be very useful brick for somebody.<br>
>><br>
>><br>
>> --<br>
>> Vitaly V. Chaban<br>
>> School of Chemistry<br>
>> National University of Kharkiv<br>
>> Svoboda sq., 4, Kharkiv 61077, Ukraine<br>
>> email: <a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a><br>
>> skype: vvchaban<br>
><br>
</div></div></blockquote></div><br></div>