One of my colleagues told me authors after acceptance can negotiate about the intellectual property (IP) rights. It is frustrating to wait for peer review long times, and after acceptance publisher asks you to agree with his copyright without any modification.
I am keen to know when is the best time to negotiate my IP rights? Can I write to the publisher when the paper is under review (or even before submission)?
I would not try to negotiate author rights before the paper is accepted, for two reasons. First, from the point of view of the editor and the publisher, it is premature and may be a waste of time (since, statistically at least, your paper has a significant chance of being rejected). Second, this negotiation could, in principle, influence the decision about whether to accept your paper (though of course it shouldn't).
Instead, educate yourself on what the publisher will allow, beforehand. Use the Sherpa/RoMEO database to know what rights a publisher will allow you, before you choose where to submit. If you choose a journal that already allows you the rights you want, then you will avoid the problem altogether.
Finally, after acceptance use the SPARC addendum to assert the rights you intend to retain.
For one story of negotiations where I didn't follow my own advice -- but things turned out fairly well -- see this blog post.
I would only submit a manuscript for publication when I was confident that there will not be any IP/copyright issues. For some types of publications, for example books, publishers will need to see the manuscript, and possibly get it reviewed, prior to making decisions about IP and royalties. I am not aware of any journal that needs/wants to see the manuscript prior to discussing IP. There tends to be things they will do and things they will not do, and it doesn't matter how good the manuscript is. The reason for dealing with IP issues (and publication fees) up front is that you do not want to waste time waiting for a publication decision that you might ultimately turn down. Further, as a reviewer, I would be completely pissed if I spend time reviewing a manuscript to see the authors publish someplace else.
At the moment, authors are at a terrible disadvantage relative to publishers with regards to this issue, since there's no collective, organized, resistance action to what publishers demand (that I know of, anyway). So you are not likely - from my limited experience, anyway - to get far with these negotiations; why should they make an exception for you? Lots of other fish in the sea.
I'd say the most important thing you can do is circumvent the copyrights issue: Publish a version of the paper which is exactly the version you initially submit to the journal on your website, university paper repository, or ArXiv, possibly with an appropriate license (e.g. see the ArXiv license page) - but not with the template used for the journal submission, i.e. as a plain-vanilla article.
Having done so, surrendering your rights via a contract witht he publisher no longer means all that much, because everybody in the world has the rights you allowed them with your free license - including yourself. The paper will thus be publicly-accessible and updatable by you without the journal being able to say anything about it. The only thing you will likely not be able to do is re-publish it in another for-pay journal etc.
