How is collision treated in gromacs leapfrog md?

User discussions
1

The collision I am pertaining to is classical mechanics definition such that when an atom or molecules collide they will bounce to the opposite direction. (Not the collision/overlap of atoms and molecules that causes crash)

Is this collision ignore, like all atoms are treated as “ghost” so they can pass through?

If not, what gromacs tool to use to determine the collision per cross section area?

Electromagnetically, I understand that gromacs accounts for Coulombic and Van der Walls interaction, which in it self sets the boundary (“aka” collision radius) of atoms and molecules where they can get repelled or attracted.

2

Yes. We have VdW interactions that act as atom boundaries, but we don’t do any other collision detection (nor does any other biophysical MD code as far as I’m aware).

In many cases, this is the desired property, e.g., in alchemical transformations or constant-pH, we want to have “dummy” atoms that are present in the topology but don’t have any (non-bonded) interactions.