From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 19 2014 - 02:25:49 CDT
If there's water between the groups you calculate the electrostatic forces between, you may want to use PME, at least because without, the water will not be able to generate bulk phase properties which does of course generate a different screening than ordered water layers.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Fotis Baltoumas
> Gesendet: Mittwoch, 18. Juni 2014 19:59
> An: NAMD mailing list
> Betreff: namd-l: Should PME be used for electrostatic interaction
> energy calculations?
> Dear NAMD users,
> Having performed a number of MD simulations on protein-protein
> with NAMD, I am currently attempting an evaluation of interaction
> values with VMD's NAMD Energy plugin. In my simulations I defined
> boundary conditions and used the Particle Mesh Ewald method for full
> My question is: should I also use PME in the calculation of
> 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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