I should probably withdraw my question. I did some tests on a smaller system, i.e., ligand in a cubic water box and the free energy differences between (1.5, 2) and (0.5, 1) I got are within 1KJ/mol, which might be OK for the single precision gromacs anyway. In the case of the protein complex, it appears that I might have driven the system out of its proper equilibrium.
On Mon, Jul 26, 2010 at 12:00 PM, Ilja Khavrutskii <[email protected]>wrote: > 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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