On 07/07/16 17:51, gozde ergin 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?
Just add a Hydrogen and update the topology. For sure you won't have
100% of COO- if you have many. As Naga mentioned you have to check
surface propensity and compare it to experimental data if you have any.
This - again - is modulated by the charge state.
The only way to do this kind of calculations in a meaningful way is by
doing series of calculations as I alluded to. Just a single calculation
can be a lucky shot.
On 07 Jul 2016, at 17:11, David van der Spoel <sp...@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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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