[gmx-users] RDF

André Farias de Moura moura at ufscar.br
Sun Jul 19 02:26:35 CEST 2015

you cannot predict solubility using the radial distribution of solvent
molecules around a single solute, single molecules just cannot aggregate
into a separate phase, so your system is too simple to provide the
information you want. even if you succeed in the thermodynamic integration,
it will provide you information about the transfer process of a single C60
from vacuum to the aqueous solution, but you would not be able to know
whether or not two or more C60 molecules would aggregate and would
eventually lead the system to a phase separation.

I'd suggest you either performing an equilibrium MD with a very large model
system with plenty of C60 molecules or an umbrella sampling simulation
using just a pair of molecules. In either case you would be assessing the
correlation between at least two C60 molecules and different PMF profiles
should provide sound arguments regarding the stabilization of the
hydrophobic solutes by the SDS molecules.

you might want to take a look at our recent paper and references therein:

de Moura et al., Thermodynamic Insights into the Self-Assembly of Capped
Nanoparticles using Molecular Dynamic Simulations, Physical Chemistry
Chemical Physics. 12/2014; 17(5). DOI: 10.1039/C4CP03519D

On Sat, Jul 18, 2015 at 7:08 AM, soumadwip ghosh <soumadwipghosh at gmail.com>

> 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
> India
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

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