This is completely unrelated to your box and your trajectory. correl can be used for energy related analyses, and by default calls the update routine to have various lists filled. Since in your case there are no coordinates present the error message you see is issued. You correctly added the noupdate keyword to avoid this; you could also have read in coordinates prior to entering the correl module, but the noupdate method is faster and cleaner.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden