Including a note to reviewers in a submission

When resubmitting a paper after rejection, many journals require the authors to provide a detailed response to reviewers, whether or not the paper is going to be assessed by the same reviewers.

Therefore, instead of including a note to explain the change, include a complete response to reviewers, even though the journal you are submitting to does not require it. It would be useful even if the reviewers are not the same, because it's quite likely that new reviewers will receive the initial comments.

Even if you don't call it a resubmission, if its going back to the same journal, it is indeed a resubmission. Even after an extensive rewrite. This is a common occurrence.

I'm sure as part of the application they will ask if you have previously submitted this work to this journal and ask for the manuscript number. In doing so everyone will know its a resubmission. It will probably go back to the same editor who will obviously recognize the work. And probably back to the same group of reviewers.

This means that you include with it, a response to reviewers. If the comments no longer apply due to the rewrite, then simply state that as your response.

The hard part will be convincing the editor that your paper is worth another look. In your cover letter you tell them how helpful the reviewers comments were and that you made significant changes to the software and the manuscript text to address the concerns. If you ignore the fact that your work was previously reviewed they might just reject it based on that. You want to make it easy for them to accept your work, not hard.

Including a response to reviewers makes your submission stronger, not weaker.

If this is not a resubmission you do not need to add any note. The paper should be self-standing and if these parameters are not used than there is no need to mentioned that they were in the previous model. The only parameters of interests are the ones being used, unless you are doing a comparative study or improving upon a previous model, in that case you would have to explain why you are not using these parameters. As long as you support all of your parameter choices you do not need to explain what you did before.

If you submit to the same journal after having received permission from the editor, than briefly state the main changes you have made, but again, the paper should be self standing.