SEARCH Articles Figures Tables Multiple threads in NAMD 2 allow the integration algorithm to be expressed sequentially as a single function. This function, shown illegibly at left, runs in sequencer threads associated with home patches. A similar function running in a controller thread on the master node communicates with the sequencers to deal with output and global calculations. Compute objects execute in the larger stack space of each node s main thread. [Publishers Imprint] [Publishers Imprint]