Should PME be used for electrostatic interaction energy calculations?

From: Fotis Baltoumas (
Date: Wed Jun 18 2014 - 12:59:16 CDT

Dear NAMD users,

Having performed a number of MD simulations on protein-protein complexes
with NAMD, I am currently attempting an evaluation of interaction energy
values with VMD's NAMD Energy plugin. In my simulations I defined periodic
boundary conditions and used the Particle Mesh Ewald method for full
My question is: should I also use PME in the calculation of electrostatic
interaction energy, or should I use the default settings, and calculate
with Coulomb's law and the defined cutoff? I have attempted both and,
although for some complexes the results are similar, in other cases the
changes are dramatic. For one particular example the results are:
Electrostatics without PME: -26.22 kcal/mol (Std. Dev.=10.16)
Electrostatics with PME: -204.58 kcal/mol (Std. Dev.=10.53)
In your opinion, which value should I trust as "biologically relevant"?
Can the PME result be interpreted as the influence of distant charged
groups to my complex, or should I use the non-PME result instead?

Thank you,
Fotis Baltoumas

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