[gmx-users] Re: pKa calculations using gromacs, final summary

Markus O Kaukonen mokaukon at cc.helsinki.fi
Thu Sep 16 10:11:08 CEST 2004

Hei Kaikki,

To summarize what I learned about pKa calculations using (partially)

1) An idea for calculating pKa values is to use method introduced by
Ullman et al (J. Biol. Inorg. Chem. v7 pp632-639 y2002) using
gromacs insted of MEAD. Deprotonation free energy is calculated
by some QM program in vacuum.

2) The role of gromacs would ONLY be in calcuting solvation free energy
difference AH and A- (see fig 2 in J. Biol. Inorg. Chem. v7 pp632-639
y2002,vertical lines). I'm not sure is it better to make protein and 30000
waters to disappear or calculating deprotonation energy in vacuum using

3) In free energy calculation with cubic periodic boundary condidion the
gromacs simulation cell can have total charge  -1...+1.
The error here is propotional to (total charge)^2 and
1/(simulation cell dimension).
In 'big' systems with high dielectric constant this error is small (<
1kcal/mol). See :J.Chem.Phys v109-pp10921-10935-y1998
So I'll forget this error.

4) Force field related errors can be high (perhaps even tens of pKa
Non-polarizable force fields introduce errors.
See JACS v126-pp4167-4180-y2004

Terveisin Markus

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