[gmx-users] RDF

soumadwip ghosh soumadwipghosh at gmail.com
Sat Jul 18 12:08:52 CEST 2015

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.
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

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