Hello halfcard,

It is not a silly question. The program's inner loops compute the influence of close segments of the protein strand. Usually this does not change much so the speed is relatively constant. Every once in a while, the configuration changes radically during a work unit. If this happens, then there may be many more close segments and the program slows dramatically. Or there may be fewer and the program speeds up. But it usually runs at an almost constant speed so you can quickly judge about how long the work unit will take to process.

mycrofth