For any other Linux newbies who are doing this too tired to think (like I was)...

After downloading the new foldtrajlite.gz to your /distributed folding directory:

1) go to your df directory, and stop the program (rm *.lock)

2) cp foldtrajlite foldtrajlite.bak

3) gzip -d foldtrajlite.gz (allow it to overwrite)

4) chmod 777 foldtrajlite (so the dang thing will execute)

5) start as you normally do (probably ./foldit)