Decision letter: disagreed with few comments I received the decision letter for the manuscript I submitted to one of the top journal in the area of network security. The editor recommended the publication of article after minor revision but I disagree with few arguments made by a review and also highlighted by the editor in his own recommendation. 
I know it is acceptable to disagree the reviewer's comments but in my case editor also emphasized same argument which is made by the reviewer.
The reviewer and editor appreciated the performance evaluation we made in article but also asked for adding the simulation. Even though we already implemented the scheme in an automated protocol analysis tool, presented the results and discussed comprehensively. 

I am a bit confused because at this stage I don't want to miss the golden opportunity of publishing my work in a top notch journal. Maybe I am misunderstanding what exactly editor want to ask. I decided to write an email to editor but my colleague stopped me and said it will not give a positive impression. 

What should be my next step?


Implement the protocol scheme in another tool (which in my opinion is strange thing)?
Submit a response with my revision that addresses the rest of the arguments and explains why I disagree with few comments (which might push our article for another cycle of revision or can be rejected)?
Send a personal email to the editor asking for clarification (which might make a poor impression on the editor)?
Something else?
A general principle that may increase your chance of acceptance is as follows: the reviewer is always right.

Of course, this does not mean that you cannot actually disagree with the reviewer. But at least for your answer letter, you should package your disagreement so that it can be understood as agreement. For example:


If the reviewer criticizes the lack of a performance experiment that you actually described in your draft, say "We agree that a formal validation alone would be insufficient to show the benefits of our technique. In fact, our previous draft already contained a section describing its implementation in a protocol verification tool and a simulation based on that implementation (Sect. X). However, we see that the structure of the paper was such that this section could easily be overlooked. In the updated submission, we have improved the structure of the paper as follows: (describe small changes)"
If the reviewer critizes the lack of a usability experiment (because you have concentrated on performance experiments), say: "We further agree that usability is another important concern of XYZ schemes. While the current submission focuses on the performance aspect, we have updated the Future Work section to give an outlook on planned user studies."