QM/MM MD and the qmParamPDB file

From: Agisilaos Chantzis (agisilaos.chantzis_at_gtn.ai)
Date: Wed Aug 15 2018 - 07:48:40 CDT

Dear all,

While running QM/MM+MD trajectories with NAMD and ORCA I have noticed
that for each force calculation cycle the ordering of the QM atoms in
the ORCA input file are changing. Although this seems not to alter the
results (the molecule seems as it should be) I was wondering whether in
a series of sequential QM/MM+MD jobs (e.g. minimization, annealing,
equilibration etc) the PDB file specifying the QM atoms (the qmParamPDB
file) should be the same in all configuration files or has to be changed
to reflect the numbering of the QM atoms at the end of the previous run.

I understand that for jobs without bonds being cut due to the QM/MM
partition of the system this atoms reordering should not have any effect
because the QM part will always remain the same, but what about the
general case of cutting through bonds?



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