Could atoms change parameters on the fly?

[Wei Lu]

In CustomNonBonded force, we can specify the parameters for each atoms. But If I want to simulate a possible reaction: when two atoms come close enough, they react to each other, how can I change the parameters after the step the reaction happened. It will be great if OpenMM can support this.
Thanks.

[Peter Eastman]

You can call setParticleParameters() on the CustomNonbondedForce to set the new values for the parameters, then call updateParametersInContext() to copy the values to the Context. This is a slightly expensive operation, so you don't want to do it every time step, but occasional updates are fine.

[Wei Lu]

Can I update the parameter when some condition are met. for example, when two atom are close to each other and their total kinetic energy is larger than certain threshold?
Thanks.

[Peter Eastman]

Not automatically. You would have to write code to check for that condition. That again involves overhead, so you'll want to limit how frequently you do it.