[gmx-users] Problems with CO2-water simulation

[sujithkakkat .]

Dear all,

        There is something which I missed to include, which I think is
adding to the confusion regarding the positive energy values.

The OPLSAA topology of methane which is available in Dr Justin Lemkul's
Gromacs tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/02_topology.html)
 , when simulated with TIP4P water gave negative energy values. Whereas,
the OPLSAA model of CO2 which is available in the same tutorial  (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/Files/topol.top)
, when simulated in TIP4P water gave highly positive potential energy
values just like the EPM2 model which I am using for CO2 in my simulations.

       This is very confusing since I believe CO2 (even as a CO2 molecule
rather than the carbonic acid form) would find itself more comfortable in
water compared to the CH4 molecule. But the energy values shows the
opposite.

     I found an example of CO2-water simulation in*
http://verahill.blogspot.in/2012/01/gromacs-carbon-dioxide-in-water-example.html
<http://verahill.blogspot.in/2012/01/gromacs-carbon-dioxide-in-water-example.html>
* , which when followed gave negative energy values. But I seriously doubt
the Lennard Jones parameters used of CO2 (eg; C6 and C12 for CO2 carbon are
assigned the values *2.5438e-1*  and *2.0478e-4)* , which the OP claims to
have obtained from *http://pubs.acs.org/doi/full/10.1021/jp062723w
<http://pubs.acs.org/doi/full/10.1021/jp062723w>*  . I think that the C6
and C12 values were not calculated correctly since they do not agree with
the sigma and epsilon values given in the reference article.

      Kindly give your comments.

Regards,

Sujith.

On Wed, Dec 10, 2014 at 10:15 AM, sujithkakkat . <sujithks58 at gmail.com>
wrote:
>
> Thank you Tsjerk. I found the paper, I will read it.
>
> Sujith.
>
> On Tue, Dec 9, 2014 at 11:52 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
>> Hi Sujith,
>>
>> I thought it's an interesting topic and googled for pressure dependence
>> of carbonic acid equilibria. I found a paper from Culberson and Pytkowicz
>> from 1968 that may be of interest. It seems I was right that the
>> equilibrium shifts towards HCO3- at higher pressure. However, even at 1 atm
>> the actual amount of CO2 appears marginal.
>>
>> Cheers,
>>
>> Tsjerk
>> On Dec 8, 2014 11:11 AM, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:
>>
>>> Hi Sujith,
>>>
>>> I don't know the work. But it would be my concern with a study like
>>> that. It should be justified explicitly.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Mon, Dec 8, 2014 at 11:01 AM, sujithkakkat . <sujithks58 at gmail.com>
>>> wrote:
>>>
>>>> Dear Tsjerk,
>>>>
>>>>     Thank you for the reply. Don't you feel that reported works using
>>>> this
>>>> model of CO2 and water for NPT simulations has ignored this very
>>>> important
>>>> existence of  HCO3-/H3O+. I mean the works which treated dissolved
>>>> carbon
>>>> dioxide as CO2 molecules swimming around . I guess they have taken it
>>>> for
>>>> granted that the HCO3-/H3O+ system serves as a CO2 reservoir and that
>>>> the
>>>> process (I am not sure of the details) of generating CO2 happens at a
>>>> rate
>>>> that is in no way a limiting factor for the rate of the actual process
>>>> they
>>>> intend to study. If this not the case, I doubt the validity of such
>>>> results.
>>>>
>>>> Regards,
>>>> Sujith.
>>>> --
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>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>>
>