Hello Ira
Rosetta.exe does incremental saves during the folding process so you will only lose the work completed up to the last save point which is always less than 1% usually somewhere between .01% and .03%

Graham's explanation is correct. Each work unit requires about 125 - 500 fold predictions. Each time Rosetta completes a fold prediction, it stores it in the work file. When Rosetta shuts down, it loses the calculations for the current fold prediction being worked on. When it restarts, it checks the work file, then begins the fold prediction again. If something corrupts the work file, then it returns that fact and downloads a new work unit from the server. Manually exiting the program has the same effect as rebooting. In either case, a small amount of computational work is lost, but as long as the work file is undamaged, Rosetta will pick up again at the start of the incomplete fold prediction.

mycrofth

Yes, sometimes the save does not occur for quite a few minutes, but that does not happen very often. In any case, the agent and the project program are designed to be substantially unaffected by shutdowns, power offs, etc. If you REALLY want to save every last second of work, you could use Standby or Hibernate instead of Shut Down.