I have read an article that says that the true nature of Amalek is denial of the existance of G-d. Does that mean that atheism and being Amalek are equivalent? I am Jewish and I strongly identify with Jewish people. At the same time, I consider myself an atheist, although sometimes, I have doubts. Does it mean I am Amalek? And if I am, do the commendments regarding Amalek apply to me?

Don't worry; no one is going to wipe you out… The article you read meant that the notion of denial of G-d is an Amalek trade, and one who is an atheist (a "real" one - not just an ignorant) is following the Amalekian tradition in not believing in G-d. Amalek has another main character trade – cruelty and hatred of the Jews, you don’t share any of those and therefore are exempt from the Amalek destiny…