[gmx-users] RDF

[V.V.Chaban]

Search for my papers "Vitaly V. Chaban". You will find many papers
determining solvation/solubility, where it is described how solubility
can be obtained from atomistic simulations.

RDF alone is not a proper descriptor. However, if you plot COM-COM RDF
for C60, you will get some solubility related information (but not
numerical solubility).

In my personal opinion, even with what you call binders solubility of
C60 is water is small. You will not be able to record it using small
MD systems.

Best of luck.




On Sat, Jul 18, 2015 at 7:08 AM, soumadwip ghosh
<soumadwipghosh at gmail.com> wrote:
> Dear all,
>             I have attempted to show the dynamics of a C60 molecule in
> presence of aqueous soluble binders. I am using GROMOS53A6 force field and
> SPC/E water. I took the pdb as well as the itp file of both from the ATB
> server. I ran simulations using GROMACS 4.5.6 of fullerene both in presence
> and absence of the organic binders for 70 ns. In order to see whether
> fullerene becomes water dispersible or not I have planned to to calculate
> delta G solvation for both the cases using the thermodynamic integration
> method. But as of now, if in presence of a binder fullerene is more water
> soluble as compared to its pristine form this should be reflected in the
> RDF calculation between fullerene center of mass and Oxygen atoms fro water
> but as you can show in the link below, the reverse thing is happening.
> Link
> <https://drive.google.com/file/d/0B7SBnQ5YXQSLVFY0MEItUTAzY1E/view?usp=sharing>
> Is there something wrong with my approach. FYI I took 8 SDS binders which
> wraps around the fullerene molecule. I think I am missing out something
> very trivial.
>
> Any kind of help will be appreciated.
>
> Soumadwip Ghosh
> Research Fellow
> IITB
> India
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