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.
Pulling a Nanowire...
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John Chodera
- Posts: 53
- Joined: Wed Dec 13, 2006 6:22 pm
RE: Pulling a Nanowire...
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
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