Pair interaction calculations of the QM/MM system

From: Alex Balaeff (
Date: Tue Jul 07 2020 - 18:44:21 CDT

Dear NAMD community:

I'd appreciate any advice on conducting pair interaction calculations
in NAMD on a QM/MM system. My calculations reveal an apparent bug --
or am I doing something wrong?

In essence, I am attempting to calculate the interaction energy
(electrostatic and van der Waals) between a ligand (described by QM)
and a solvated protein (described by MM).

For the whole system, the energy looks quite reasonable:
E_elec = -932364.2484, E_vdw = -427.4665

whereas for pair interaction between the QM and MM parts, the vdW
component goes haywire:
E_elec = -118280.8276, E_vdw = 48861334.1618.

If I compute the self-interaction of the MM part I get:
E_elec = -932294.1036, E_vdw = -427.4665

which is reasonable again, except E_vdw is *exactly* the same as for
the complete system. Which is wrong, isn't it? because NAMD does
calculate the vdW interactions between the QM and the MM parts, so
that the total E_vdw should include E_vdw(QM-MM) in addition to
E_vdw(MM-MM). And yes, I do have the vdW parameters for the QM atoms
set up by CGenFF, and don't scale them down to zero.

The self-interaction of the QM part is crazy again:
E_elec = -118339.2930, E_vdw = 48861334.1618

which makes even less sense: the vdW interaction between the QM atoms
is simply not computed, so shouldn't it just be zero??

When I remove the ligand from my MD snapshot and calculate the energy
of the remaining part (without the pair interaction this time), I do
get reasonable values again:
E_elec = -932294.1034, E_vdw = -382.2416

However, why are these values different from those above computed for
the MM self-interactions? Shouldn't those be same values?

Any advice on this confusing situation would be greatly appreciated. I
am attaching a README file describing the problem in more detail, and
put a complete test case (including the NAMD scripts and their log
file outputs) on my Google Drive:

Thank you very much,


  Dr. Alexander Balaeff
  Polaris Quantum Biotech

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