From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Thu Apr 04 2019 - 15:05:07 CDT
Hi Atanu,
Yes, the point charges are (by default) re-defined at every step. Using the
cutoff distance, NAMD selects a "shell" of point charges around your QM
region(s).
You can provide a PDB file with a static selection of point charges (check
the *qmCustomPCSelection *keyword in the documentation) if maintaining a
constant selection is important for your particular case.
As for minimization, usually the QM energy is much greater than the MM
energy, and tends to dominate the potential. Not knowing more about your
case I could only suggest running an equillibration to see what happens.
Best,
Marcelo
--- Marcelo Cardoso dos Reis Melo, PhD Postdoctoral Research Associate Luthey-Schulten Group University of Illinois at Urbana-Champaign crdsdsr2_at_illinois.edu +1 (217) 244-5983 On Wed, 3 Apr 2019 at 15:06, Acharya, Atanu <aacharya42_at_gatech.edu> wrote: > Hi there, > I am trying out the NAMD QM/MM interface with ORCA. I noticed that the > .pntchrg file is written in the qmBaseDir directory. > However, the number of pointcharges in the file is different in each step. > Is this because NAMD is writing the charges within the cutoff distance? > In my calculations, I noticed the that during QM/MM minimization the QM > energy does not go down (the MM energy does go down though). > Can someone provide some insight into that? > > Thanks a lot, > Atanu > >
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