[gmx-users] Re: pKa calculations using gromacs

Markus O Kaukonen mokaukon at cc.helsinki.fi
Tue Sep 14 10:22:39 CEST 2004

Dear All,

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.

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).

Obvious problem here is that the simulation cell is not neutral in
either AH or A-. As Professor Case kindly pointed out this can be
overcome by introducing a uniform neutralizing plasma (if I understood
correctly this is implemented in AMBER).
[Case's article:JACS v126-pp4167-4180-y2004
About uniform neutralizing plasma:J.Chem.Phys v109-pp10921-10935-y1998 ]

Is uniform neutralizing plasma impleemnted in Gromacs?
If not, where is the electrostatic potential of an ion
(phi_q(x)) in
J.Chem.Phys v109-pp10921-10935-y1998 eq. 2.14-2.15 or eq 2.18)
calculated in gromacs?
One simply would need to add a simuluation cell size depended constant
to the electrostatic potential (in case of cubic periodic boundary

Terveisin Markus = Markus.Kaukonen at helsinki.fi

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