I am still getting random freezing under FreeBSD, all looks fine when you do a ps -ax, but you have to do a kill -9 to the foldtrajlite process to get it to stop, it ignores the removal of the lock file. This happens one several machines, I get one or two every day on a group of 20 different machines. If I run Linux on the same machines the problem does not occur, and they seem to get through a set of 250 faster than the same machine on FreeBSD. This also happend on the previous protein. All machines are running with the -q flag.