it can happen because:

1. you are on a crap managed VPS ( also other users are using too much memory, and then the server overloads )
2. you have a bad coded script and it overloads because of it

how to test it?

just put a normal index.html file on the vps, and if the server load is still high then it's the VPS, then you should change your VPS. else it's your script.