Reply To: AbinitioRelax under different directories without -constant_seed -jran flag

[Anonymous]

1) What you have done here is not guarunteed to produce identical or non-identical models – it depends on what seed your operating system hands to Rosetta. On many systems, jobs get the system time as their RNG seed, thus jobs started simultaneously will get the same seed. constant_seed + jran can guarantee different seeds (which is what you want). If the models are different, feel free to pool them. You can also check for yourself what the RNG seed was for a run, it should be printed at the top of the log file.

2) All trajectories are independent. So, if it runs through models 1-10, then crashes, and you restart, it checks to see 1-10 are finished and starts at 11. The only relationship between models is that the production of one model moves the RNG along, such that models 1 and 2 and 3, etc, all get different sequences of random numbers.

3) The error “NANs occurred in hbonding” is serious, but may be related to the other error “ERROR: trying to use a ‘protein’ type silent file for a non-idea l pose core.io.silent: consider using the ‘-out:silent:silent_struct_type binary’ flag”. NANs in hbonding means that something bad happened to atom placement and the hydrogen bond terms tried to divide by zero (or something similar), I can’t diagnose it more specifically. The second error indicates that you’re using a non-ideal pose. Are you starting from a model? Did you idealize it with the idealize application?

4) The “max cycles exceeded” warning is not good, but not terrible. It most likely means that your pose found its way into a region of space where there’s a small error in the derivative of one of the energy functions, and the minimizer couldn’t minimize it properly because the derivative was strange. It won’t cause a big problem. I don’t understand your question about flags.