Water wrapping in the QMMM simulations

From: Alex Balaeff (abalaeff_at_polarisqb.com)
Date: Mon Dec 14 2020 - 17:27:11 CST

Dear NAMD developers and gurus:

Could those who know these details kindly advise how NAMD treats the
periodic images of point charges included in the QMMM calculations?
Say, I have a QM ligand simulated in an MM water box, and the ligand
drifts to the edge of the box. Is NAMD smart enough to include the
water molecules from the neighboring periodic cell into the MM shell
around the ligand that is sent to the QMMM calcs? Or is it not, and
one better make sure that the ligand is restrained to the center of
the cell?

If it matters, I am using a NAMD/MOPAC combo and run semiempirical QM
calcs (AM1, PM7).

Thank you all,


  Dr. Alexander Balaeff
  Polaris Quantum Biotech

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