[gmx-users] Inorganic Material Simulations

[ANAND AMITKUMAR Dharia]

Hey there,

I am interested in simulating a protein diffusing inside an inorganic
nanotube. I want to study how the diffusivity of the protein changes as a
results of the surface interaction with the nanotube. Specifically, I am
looking to understand how to define a force field for the nanotube and
protein/solvent interactions. Additionally, I want to know if I can
restrain the atoms of the nanotubes only and use these atoms solely for
polarizable effects within the simulation space. I have looked into the
drude oscillator force field and am trying to understand how I can
implement this model. Please let me know any advice or point me to some
documentation of how I can approach this.

Thanks,
Anand Dharia
University of California, Berkeley