I’m having problems trying to understated, what are MD5. I have three questions.
Can any one explain these to me?

1) What is a "collision"?
2) If a collision was found in MD5 what would it mean for an IDS like
tripwire that relied on MD5?
3) How can we fix this problem? (i.e. Are there alternatives to MD5
which could be applied?).

Here is an example of a collision: http://www.tcs.hut.fi/~mjos/md5/
Basically it is 2 file with the same md5 sum.

It means that not all results given by a programs that use md5sum are 100% accurate. I have an antivirus scanner for Windows (Computer Assoc. eTrust AV) that probably uses a method similar to md5summing to find viruses. There is a particular file that it finds to be a virus on every computer here at work. I have researched that virus and am posititive it is not the virus it claims to be. It's mearly a false positive.

Here's another article that might help.
http://www.cryptography.com/cnews/hash.html

I found all of these on google. Try that, too.