Hi, I have seen previous posts on the sc_alpha/sc_power, but they did not answer my question: why does the free energy of an alchemical transformation (the work that it takes to change state A into state B in a single leg of a thermodynamic cycle) change when I change (sc_alpha, sc_power) from (1.5, 2) to (0.5, 1). The A and B Hamiltonians should be identical at lambda 0.0 and 1.0 regardless of the values of (sc_alpha, sc_power), I think. I see differences of 40 KJ/mol in the work values averaged over 8 independent simulations that are converged to at least within 5 KJ/mol for each set of (sc_alpha, sc_power) (2 ns MD in each TI window, NPT). I am using GROMACS 4.0.5 single precision run in parallel. My system is periodic with a protein, ligand an cubic water box and I have dummy atoms only in the state B. I would appreciate any hints into this. What am I missing that would explain the difference of 40 KJ/mol for just changing parameters from (1.5, 2) to (0.5, 1). I am specifically asking about the single leg work (deltaG), not the whole thermodynamic cycle (delta-deltaG).
Thanks, -Ilja
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