[gmx-users] dielectric constant effect on protein, dna, water interface

[Sarath Chandra]

Fellow users,

I am working on a Protein-DNA complex and I have a question regarding the
electrostatic interaction energies calculated at the interface of protein,
DNA and water. I am using amber99sb+parambsc0  forcefield for my system
with TIP3P water simulated using gromacs4.6.4.

I understand that the additive forcefield does not capture polarizibility
well. I have already referred to articles on PME but it is not clear if the
PME takes into account the dielectric constant change at the protein, DNA,
water interface. During the electrostatic forces calculation is this
captured by calculation of local dipole moments on fly? This is critical to
understand the effect of protein on DNA structural properties.

I look forward to your reply.

Best regards,

Sarath