Dear all,

Could anyone tell me please how I can do (simulate) ultrasonication?

In addition, is there any option in mdp file to apply force to the system?

Best regards

there used to be a non-equilibrium option,
search for the term cos-acceleration in the mdp file documentation!
i believe, though, that this option is depreciated in the latest gmx version.

Dear Michael,
Many thanks for your response.

Could you please tell me how I can choose the proper value for cos-acceleration?

Does it depend on the size of the box?


short answer, i don’t know … but if you are talking about ultrasonication - whatever device or exptl setup you try to emulate - this should come with a certain frequency in inverse time units (kHz) … ideally this would be the frequency to use,
but i am not sure how to convert that to gmx input, as here you are supposed to provide an amplitude - the documentation is not very there, at least for my limited understanding …