[gmx-users] Sigma and epsilon parameters for water and graphene atoms

[Mark Abraham]

Hi,

On Sat, Jul 30, 2016 at 5:43 PM soumadwip ghosh <soumadwipghosh at gmail.com>
wrote:

> Dear all,
>              I have recently simulated the interaction between graphene and
> nucleic acids under aqueous conditions. In one of the reviews of my paper,
> I have been asked to detail the  interaction between graphene atoms and
> water (standard Lorentz-Berthelot combination rules for epsilon and sigma).
> Are they referring to the sigma and epsilon values in the ffnonbonded.itp
> file?


I guess so


> My carbon atomtype for graphene is CA and the water model is TIP3P
> and I have used CHARMM 27 force field for MD simulations.I guess I need to
> dig out the individual sigma and epsilon values for each atoms and then
> calculate the combinations (such as sigma CO and epsilon CO). Am I guessing
> it right? Any kind of help will be appreciated.
>

If you want to understand what you're doing, make a test system with two
atoms at a known distance, pick atom types that are of interest, make a tpr
and do mdrun -rerun your-configuration.gro

Mark


>
> Thanks and Regards,
> Soumadwip Ghosh
> Senior Research Fellow
> IITB
> Mumbai
> India
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