How to set up a system containing an acid molecule on air -water interface?

User discussions
1

Hello everyone. I am very new to GROMACS and molecular dynamics in general and I want to simulate an acid at the water-vapor (or vacuum) interface. I am curious about how exactly can be set up this system.
What I did,

  1. Created a simulation box containing an air-water interface.
  2. Minimized the energy of the system and equilibrated it.
    now i want to place an acid molecule on the interface.
    Can anyone please suggest me know how should I proceed?

Thank you.

2

@Shivangi hello can you tell me how did you set your system up? and how do you generated air? is there any good reprenstation for air
?