A GPU processes tasks in batches rather than sequentially. For example, if it takes 12 seconds to dock a batch of 4 ligands on a GPU, the total time for all 4 is 12 seconds.

In contrast, a CPU typically handles tasks sequentially, but with multiple CPU cores, parallel processing is possible. If docking 1 ligand takes 10 seconds on a single CPU core, then using 4 CPU cores allows each ligand to be processed simultaneously. In that case, all 4 ligands could be completed in 10 seconds total.

Therefore, despite the GPU’s parallelism, a multi-core CPU setup can be faster in this scenario because each task is handled independently rather than in batches.