From: Alex Balaeff (abalaeff_at_polarisqb.com)
Date: Thu Mar 18 2021 - 12:17:11 CDT
Dear NAMD developers and QMMM gurus:
Could you kindly advise what terms the printed out NAMD electrostatic
energy includes in a QMMM simulation?
Here's the link to an "ultimate" example:
where the system consists of a QM ligand only and no classical part.
>From the NAMD QMMM calculation (cf. energy_ligand_only_1.{namd,log})
it appears that ELEC = QMENERGY - PMECORRENERGY. So... what is
PMECORRENERGY?
The NAMD QMMM paper (nihms947830.pdf) gives a vague explanation that
"corrections are calculated to subtract from the PME forces all
interactions already calculated by the QM package between QM-QM atom
pairs, and by NAMD QM module between QM-point charge atom pairs". The
latter part is absent from my test system (no point charges!) so only
the former part remains. So it sounds like the PMECORRENERGY could be
the PME interaction energy between the QM-generated point charges.
However, when I literally substitute those charges into my PSF file
(Ligand_test.psf_new) and redo the calculation with the ligand as a
classical MM system, the electrostatic energy comes out different from
PMECORRENERGY (184.55 kcal/mol vs. 111.05 kcal/mol, respectively: cf.
energy_ligand_only_1.log and
energy_ligand_only_MM.log).
Moreover, when I redo the MM calculation without the PME term (and
with a large cutoff, to get the actual all-with-all interaction), I am
getting the electrostatic energy very similar to the PME one (184.53
kcal/mol: cf energy_ligand_only_MM_noPME.log) Which means that the
electrostatic interaction with the ligand copies is minuscule and the
PMECORRENERGY term cannot be that, either.
So, if someone could kindly explain what the PMECORRENERGY term
includes, that would be much appreciated :-)
Thank you very much,
Alexander.
-----
Dr. Alexander Balaeff
Polaris Quantum Biotech
https://urldefense.com/v3/__http://www.PolarisQB.com__;!!DZ3fjg!tLywrT9Ies8ueIfslWWFnhAUUlorpX5Uy8hCjwaJkBaf6QG-NoUGlK73B2-1KqG5pQ$
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