I am trying to run an all-atom refinement of candidate conformations with the Relax application. I found the manual page listing all of the relax parameters, however I am looking for guidance as to what these values should be. Can someone point me to a paper that describes the usage of the Relax application?
Specifically I am wondering about the following:
1. what is the relax:min_tolerance parameter used for?
2. how should I prioritize adding cycles to the three stages? That is, if i want to increase the time my refinement runs for should I primarily increase just the stage 3 cycles or should I increase stages 1 & 2 as well?