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Recently, I have submitted a paper to a high rank journal where I have considered a physical system, and applied a mathematical technique. In order to perform this technique, I have considered some approximations, and the results obtained extended previous results. However, the approximations used in the paper are valid among different approaches in the field, being used in different papers. From this perspective, I know how to response to the referee critics, with evidence from the scientific literature. The question would be if it is appropriate to respond to the referee critics and to motivate in the article the mentioned limitations, or to submit to a new journal. I mention that in the previous published papers by our group the referees didn't used the word rejection, and have pointed to a major/minor revision. Note that the reviewer report does not says anything about the invalidity of the results, only that they are limited by the approximations used in order to treat the system mathematically and not numerically.

Update: the paper was finally rejected. The reviewer's comment from the second round were not so negative, recommended a major revision, but the editor decided to reject the paper.

New update: the referee comments from the second journal have arrived, the paper has a high chance of being accepted after a major revision. Eventually the paper was accepted.

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    Usually, you should receive not just the referees’ reports/recommendations, but also receive the editor’s decision on whether to accept or reject. What was the editor’s decision for this paper?
    – PLL
    Commented Oct 22, 2016 at 13:57
  • @PLL it was standard, "the present manuscript is not suitable for publication"
    – Nikey Mike
    Commented Oct 22, 2016 at 14:13
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    I would like to say something personal and probably off-topic. Long time ago, the girl I was chasing after said "You're not suitable for me". It took me a while (a very painful while) to realize that she was rejecting me.
    – Nobody
    Commented Oct 22, 2016 at 15:01
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    If the editor says "not suitable for publication" then go on to another journal. The important thing for you is what the editor says, not what the referee says.
    – GEdgar
    Commented Oct 22, 2016 at 16:00

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Unless you have some indication from the editor that your paper is still going to be entertained if you resubmit, I would not send it back to the same journal. Most of the time, the editor will provide you with a bit of additional guidance, besides what is stated in the verbatim referee report. This should be your guide to whether resubmission would be worth the time. If the editor suggests that you might be able to overcome the referee's criticisms, and you think that you can, then go ahead and make the changes and send it back. If the referee says the paper is being rejected, then you ought to start looking for a different publication venue.

If the editor's own comments do not address the status of the paper specifically (and this does happen; the Physical Review journals often send the author the referees' reports without any additional guidance from the editor about whether acceptance is likely the next time around), I would presume that editor is tacitly concurring with whatever recommendation is in the reviewer's report. In your case, if the editor is effectively silent, I think you should just move on to another journal.

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