I was reading the article “Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand” (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132508) in which the new low resolution mover “Transform” was implemented as part of the RosettaLigand protocol, replacing the old “Trans/Rot” Mover. One of the most impressive achievement was done regarding the efficiency of the protocol. In figure 3 (see link above) there are kernel density plots showing the distribution of time to produce a single trajectory, for 4 different protocols. The Transform/MIN protocol shows a normal distribution centered approximately around 10 seconds. This could allow for really fast exploration of binding poses, given that an average trajectory will only take 10s.
When I test the aforementioned protocol my system took in between 500 to 600 seconds to complete each trajectory (which is approximately a 60 times increase). Is it possible that some options are making my runs more slower than the ones reported?
My options file looks like:
The xml protocol file is the exactly the one in the directory:
The trajectory time is independent of the -ex1 and -ex2 flags. I repeated the test commenting them out and the results are the same.