Negotiating with journal publishers about intellectual property of the paper? 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.