Periodically, the core writes data to your hard disk so that if you stop the client, it can resume processing that WU from some point other than the very beginning. With the Tinker core, this happens at the end of every frame. With the Gromacs core, these checkpoints can happen almost anywhere and they are not tied to the data recorded in the results. Initially, this was set to every 1% of a WU (like 100 frames in Tinker) and then a timed checkpoint was added every 15 minutes, so that on a slow machine, you never lose more that 15 minutes work.
As proteins become more complex and run longer, it is better to have more frames in a WU so that you don’t lose so much progress if you have to restart – – hence WUs that have 400 frames instead of 100. That still doesn’t take the speed of the machine into account. A fast machine completes a frame in a few minutes while a slow one may take hours, and the donor with the slow machine still doesn’t want to lose 99% of those “hours” yet the fast machine doesn’t really want the overhead of writing the checkpoints every “few minutes” – – and neither of them wants the upload time associated with results containing many frames.
Starting in the 4.x version of the client, you can set the 15 minute default to another value (3-30 minutes).
Thanks to Bruce Borden for this FAQ entry.