| 4:43:22 PM PDT - Thu, Oct 17th 2013 |
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Hi,
I just need a confirmation that the free energy output from FEP calculation contributes to just
deltaW_solvation part as in http://nwchemgit.github.io/index.php/Release61:QMMM_Free_Energy, without the deltaW_QMinternal included. Or is it another way around? I have taken a look into the source code from https://github.com/jeffhammond/nwchem/blob/master/src/qmmm/task_qmmm_fep.F (around the line 675-700) and it's likely to be the first speculation but would need someone to confirm this too.
Also, to obtain a complete plot of free energy, here is what I understand. Because the free energy calculation is done between 2 beads (states), say A and B, B and C, or C and D (suppose we have 4 beads A,B,C and D). If I want a complete plot of free energy respect to state A (set to zero), do we simply calculate
deltaW_a,b = deltaW_QMint_a,b + deltaW_solv_a,b
deltaW_a,c = deltaW_QMint_a,c + deltaW_solv_a,b + deltaW_solv_b,c
deltaW_a,d = deltaW_QMint_a,d + deltaW_solv_a,b + deltaW_solv_b,c + deltaW_solv_c,d
?
Any idea would be greatly appreciated.
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part. I also think your scheme is reasonable to calculate the energy difference between state A and D.