[gmx-users] residue titration w/ FEP

[David L. Bostick]

Thanks for the suggestions ..
>
> The workaround that I have used was:
> 1)state A = H atom
> 2)state B = DUM atom
> 3)DUM atom has C6 and C12 = 0.0, but has some mass (you can put this value in
> your protein.itp file in the [ atoms ] section)
> 4)the bonded interactions remain the same
> 5)you will have to add in the [ pairs ] section or directly in the ff*nb.itp a
> null value for the 1-4 interactions with DUM atom.
>

I am unsure of how gmx perturbs from a real atom to a dummy atom.  I
actually tried modelling the glutamatic acid COOH using a dummy atom for
state B, COO-DUM. It appeard that the constraint I built in for the dummy
atom in state B, held for state A as well.

Originally, I tried perturbing LJ, coulomb, and mass going to zero for the
proton without a dummy atom.  This, I feel, is the most physical thing to
do. I was able to run a stable simulation for each window from lambda=0 to
lambda=0.95 -- almost all the way to the end.  I am tempted to just
extrapolate lambda=0.95 with a curve fit and integrate.  This would
represent a true perturbation.  I left all bonded interactions with the
proton in the topology of state B in order to keep the proton from floating
around, unconstrained.  My reasoning here is that, with zero mass, all bond
and angle terms (with no force exerted on them from the massless particle)
should be in their equilibrium position and thus make no contribution to
the total energy. However, when lambda approaches 1, the same problem
results as without the bonded terms, even though the particle has no mass,
because the bonds and angle terms can exert no force on the particle.

I just don't know if the dummy constraint holds for state B only.  I think
gmx treats the particle as if it were a dummy for the whole range of
lambda.  If I am wrong please let me know...

Thanks,
David

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