I'd like to ask few questions related to ddg_monomer application:
1) When I set number of iterations to 50 (-ddg::iterations 50), the average energy in ddg_predictions.out file does not correspond to the arithmetic mean of the individual runs in the full output file. When I set number of iterations to 20 (other settings is the same) everything is OK.
2) Calculation of double-point mutants produces different energies depending on the order of the mutations (A1B, C2D has different energy from C2D, A1B - up to 1 kcal/mol). How does this application functions? How should I run calculation on multiple-point mutants?