QM atoms outside the PBC boundary in QM/MM calculation

From: Haohao Fu (fhh2626_at_gmail.com)
Date: Sat Sep 02 2017 - 21:55:26 CDT

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Dear NAMD developers,

I want to perform a semi-emperical BOMD in NAMD with MOPAC. It seems the
only thing that I should worry about is the non-periodicity of the QM part.
When a QM atom moves outside PBC boundary, it emerges immediately from the
other side of the PBC, making MOPAC confused. Since MOPAC support PBC by
defining three "translation vectors", I can ask NAMD to output:
Tv xxx 1 0.0 1 0.0 1
Tv 0.0 1 xxx 1 0.0 1
Tv 0.0 1 0.0 1 xxx 1
in /0/qmmm_0.input by revising the source code. Then the semi-emperical
BOMD is Rigorous.

Am I correct? Do I miss something?

Cheers,
Haohao

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