[gmx-users] Problems with CO2-water simulation

[David van der Spoel]

On 2014-12-14 09:49, sujithkakkat . wrote:
> 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.

You could try the ones we used:
http://dx.doi.org/10.1021/ja411579b
check references within, but we also provide hydration free energy.
>
> 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.
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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>>>>
>>>>
>>>>
>>>> --
>>>> Tsjerk A. Wassenaar, Ph.D.
>>>>
>>>>
>>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se