[gmx-users] Free energy of protonation

[Gmx QA]

Dear list,

I am trying to calculate the free energy for protonating a single monomer
of oleic acid with the martini forcefield. This in preparation for other
work, and I wanted to start by reproducing what is already done.

To do this, I have defined the following in my topology to describe the
change in protonation state going from A (protonated) to state B (charged).
The martini bead type needs to change as well in this process.

[ atoms ]

; id    typeA   resnr   residu  atom    cgnr    chargeA   massA typeB
chargeB massB

  1     P4      1       OAN     COO     1       0               Qa      -1

I also have this very simple mdp file for doing the transformation

free_energy              = yes

init_lambda-state        = 1

fep-lambdas              = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0


And I am using fep-lambdas to describe the entire process. With this, I can
run through grompp and mdrun with different values of init-lambda-state,
but the output I get in each case is the same for each different simulation.


I check this by


gmx analyze -f md.xvg -ee


And I always get the same value for the average. Is there something I am
missing or not specifying properly?


Thanks

/PK