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.

3

I understand it’s a little too late for my reply. Most articles I have read on graphene/CNT suggest TERSOFF for graphene/CNT. AIREBO for graphene I have read but to me it seems like you would use AIREBO when you want to study mechanical properties of graphene (for instance stress strain relation).
I am trying to simulate a system with graphene in it and I have been thinking of using TERSOFF but I could not find (still need) a way to get the TERSOFF for graphene. Any suggestion/help is appreciated.

Thank you!

4

There are multiple variants of Tersoff in parameters for carbon in the literature. You will find several of them in the potentials folder of LAMMPS.

1 Like
5

Thanks for a prompt response.
I recently read in BNC.tersoff potential file (in lammps dir) that it contains parameters for lattice dynamics and phonon thermal transport in CNTs and graphene. I think I will use it after more research.