simtk.org

Hello,

I am simulating pulling of a nanowire using OpenMM. Currently for pulling a set of atoms I will change the velocity of a set of atoms that are at the extreme ends of the nanowire. However, this will cause the nanowire to break at a place close to the extreme ends of the nanowire. I was wondering if there would be a way to uniformly pull the atoms?

Sincerely,
Kasra.

Hi Kasra,

What kind of experiment is your simulation meant to mimic? Is it pulling in a laser trap? By an AFM tip?

If you're simulating something like pulling in a laser trap, it might make sense to create a CustomExternalForce that traps one or more atoms at one end in a fixed harmonic well, and one or more atoms at the other end of the nanowire in a harmonic well whose position is controlled by one or more global parameters. You can then change the mobile trap position as the simulation goes on, alternating between taking a few steps of dynamics and moving the trap position a bit more. There are limits to the speed at which you can pull and still have a stable simulation, but this would reasonably mimic the situation found in an optical trap.

Best,
John