MD simulation DNA+Graphene sheet in LAMMPS

LAMMPS LAMMPS General Discussion
#1

Hi everyone
Dear LAMMPS users

I want to simulate DNA+Graphene sheet, in a few steps:

  1. simulate them by considering van der walls distance while system is in equilibrium (it’s stable) after 1ns(This is the hard part I guess)
  2. Then manipulate DNA on Graphene and compare the friction force between them when Graphene sheet is one only layer and multi layers.
    How should I choose proper force_field for this combination?
    My priority is this but I am not sure:
  3. AIREBO for graphene, CHARMM for DNA
  4. TERSOFF for Graphene, CHARMM(or DREIDING) for DNA
  5. DREIDING for both.
  6. CHARMM for both.
    Any experience about my research would be appreciated a lot.

Sincerely Yours.

#2

The best way to see what can be done and what would be reasonable choices is to survey the published literature. I would not only look at studies of DNA on graphene, but would also include DNA with CNTs.
A long time ago, I helped a colleague to do some extensive studies on ss-DNA with CNTs and he used Amber parameters (rather than CHARMM) but also used Gromacs for better performance: https://dx.doi.org/10.1021/nl802645d
Since this is a well cited publication, you may also find useful information in publication that are citing it.