[gmx-users] reference on free energy with soft core electrostatics and PME?

David Mobley dmobley at gmail.com
Fri Oct 21 21:09:58 CEST 2005


I need some information about how Gromacs handles PME for free energy
calculations when sc-alpha is nonzero and the perturbation is electrostatic.
That is, how is PME handled when soft core potentials are used to turn off
electrostatics for a molecule in solution, for example? For what it's worth,
I'm using the CVS version of Gromacs 3.2 referenced here (
but I assume things are handled the same in Gromacs 3.3, which I'll be
switching to shortly.

What I'd like to see is a derivation or description of a derivation for what
it means to correctly deal with PME for this case. The recent J. Comp. Chem.
paper on Gromacs (v. 26, n. 16) states that "Differences in constraints or
in long-range interactions are
properly handled," but doesn't explain what it means to handle these
properly in the soft core case. The papers referenced in that section (one
on Gromacs 3.0, and van Gunsteren's paper introducing the soft core
potential) are similarly unhelpful.

In other words, I know the claim is that Gromacs now properly handles
electrostatics when a soft-core potential is used to turn off electrostatics
in a free energy calculation. But what does it mean to "properly handle"
this? How exactly are they handled? Again, I'd like to see a derivation (or
reference to one) or at the very least a description of a derivation so I
can work through it myself.

David Mobley
Dill group
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