Program Execution: output does not appear

["Angelo R. Rossi" <rossi@york.cuny.edu>]

Hello:

I am using a large molecular dynamics program in the following manner:

                              charmm <input.file  >output.file

The problem is that the file output.file is created, but remains empty.
 After a while, the file fills with some output but still holds back
much of it.

What is happening here?  This is the first time anything like this has
happened.  Usually, output appears immediately.  It seems as if it is
going into a buffer and not being put to the hard drive.
Please help with this.

I am using debian unstable and uname -a gives:

Linux thebox 2.6.11 #2 SMP Thu May 26 20:53:11 CEST 2005 i686 GNU/Linux

Please help if you can.

Regards,

Angelo