[gmx-users] Surface tension calculation for organic monolayer

[Evan Lowry]

Create another residue that has a missing hydrogen in the -OH group so that
your acid is COO- instead of COOH. Then add this acid along with the
protonated one in different proportions and then add enough hydrogen atoms
to account for the undercoordinated oxygens. That's one way to do it, there
could be others.

They do something similar in this paper: Javanbakht, Gina, et al.
"Molecular Dynamics Simulations of CO2/Water/Quartz Interfacial Properties:
Impact of CO2 Dissolution in Water." *Langmuir*31.21 (2015): 5812-5819.

Evan L.
Yes but my acid is in protonated form.
> On 13 Jul 2016, at 17:42, Evan Lowry <evanwlowry at gmail.com> wrote:
>
> Dr. van der Spoel is correct. If you don't take into account the
> protonation state, your calculation may likely be incorrect. The pH can
> have a notable effect on interfacial/surfactant systems.
>
> Evan L.
> Dear Spoel,
>
> I am using the protonated form of cis-pinonic acid which means head group
> is COOH.
> I tried many other surface active molecules but never manage to estimate
> the lower surface tension than water.
> Is there anyone here that did the MD simulations with surface active
> molecules on water and estimated the reduced surface tension?
> Any suggestion would be really helpful.
> I tried some other force field (GAFF, AMBER, OPLSAA) but results did not
> change.
> I am doing something wrong but I do not know what.
>
>
>> On 07 Jul 2016, at 17:51, gozde ergin <gozdeeergin at gmail.com> wrote:
>>
>> Dear Spoel,
>> Thanks for your respond.
>> For this simulations I used acids however I got the similar results when
> I used alcohol (pK values are lower than acids).
>> I doubt this error coming from the pH effects.
>> But how could i get the protonated molecules configuration?
>>> On 07 Jul 2016, at 17:11, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>>>
>>> On 07/07/16 16:06, gozde ergin wrote:
>>>> Dear users,
>>>>
>>>> I simulated three different systems in cubic box and calculated their
> surface tension as shown below;
>>>>
>>>> 1. Pure water , surface tension = 61.5 mN/m
>>>> 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m
>>>> 3.Water surface covered with cis-pinonic organic, surface tension =
> 63.5 mN/m
>>>>
>>>> For system 1 and 2, the results are almost correct however the result
> for system 3 is not correct.
>>>>
>>>> Cis-pionic is an surface active molecule and should lower the surface
> tension.
>>>> However in my simulations I could not capture this trend.
>>>> I used GAFF force field and LINCS for the constraints.
>>>> Does anyone has any idea?
>>>> Or is there anyone that calculated the surface tension for organic
> coated surfaces with GAFF force field?
>>>>
>>>> Thanks
>>>>
>>> Maybe you should consider pH effects? Since this is an acid I would
> guess part of these are deprotonated in solution, did you consider the pK?
> You probably need to mix different amounts of protonated and deprotonated
> molecules and plot the surface tension as a function of the protonation
> state.
>>>
>>> --
>>> 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
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