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I am considering applying for PhD degree. Regarding this I contact many professors to see if they are accepting new students or if I am a good fit for their research group. The responses will be different.

For some of them, if lucky, they tell you the instruction, e.g. send your CV, contact me for the research you have done etc. However, you may receive a general email which most of the times means he/she is not interested in your CV. They write a general description of the application process or maybe a rejection to your request.

What should I reply back to these kind of responses from professors?

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    If you were the professor, would you like to receive a thank you note? – Eliezer Dec 8 '15 at 17:58
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    I'd be the first to encourage everyone to be more kind and polite, to send each other notes, gifts, etc., but here's something to consider: for you, the application process is an exciting process that represents an important step on the way to achieving your dreams. For a professor, getting these sorts of emails and responding to them is... just another day at the office. Not that we don't like helping people like you and sharing in your excitement, but at the end of the day, this is something that happens to us all the time. So, I'd say a thank you note really isn't necessary here. – Dan Romik Dec 8 '15 at 18:16
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I would say, write a very brief e-mail in response saying something along the lines of "Understood, thank you very much." It's probably unnecessary, but it takes fifteen seconds to write and five to read and delete.

In particular -- a thank you note has essentially no possibility of annoying the professor, at least if it is not also accompanied by some sort of request. I would say -- if you are contemplating writing a brief thank you, then you may as well do so.

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If you consider to send just a thank you email- then it is no, it would not make any impact at all. No professor cares about emails which are not substantial from prospective students. They get hundreds of those everyday.

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Yes, it is almost always a good idea to thank people for things they have done. While these professors may not be likely to take you on, you never know when you will meet them in the future, or whether they will review your work or consider you for a position.

Additionally, what you could do if they reject you is to thank them, but also ask for suggestions for another academic with whom your work might be a better fit, or any feedback on what you could do to improve your chance of success in the future.

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