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The menu.lst file has a line that looks like "password --md5 c5ae09c39ad1e0d2aa12231eea7bc5c2"

The grub-md5-crypt command creates salted, iterated md5 hashes that look more like "$1$uhYnK0$znfYd7RiEqPi9xujI03sy0"

What's going on? Is this normal? If I copy the output of grub-md5-crypt into menu.lst, will everything break?

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Yes, the two values are not equal, you would have to salt the md5 password to get a compatabile input. – Ramhound Oct 18 '11 at 16:05
The question is, why is the value in the grub configuration file not created by grub-md5-crypt? And if I put in one that is generated by grub-md5-crypt, what happens? – user56969 Oct 18 '11 at 18:33

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