Hi Ivan,
> How does Amber treat QM/MM MD with periodic boundary conditions?
> Specifically, who is the QM system replicated and its contribution
> included into the total energy? I'll appreciate if you point me to the
> literature
For semi-empirical QM/MM calculations yes the periodic boundaries are
included via a QM compatible version of the PME procedure. Please see:
Walker, R.C., Crowley, M.F., Case, D.A., "The Implementation of a Fast and
Accurate QM/MM Potential Method in AMBER." J. Comp. Chem. 2008, 29,
1019-1031.
http://www.wmd-lab.org/papers/JCompChem_2008_29_1019-1031_Amber_QMMM_Paper.p
df
For ab initio QM/MM calculations via the EXTERN interface periodic
boundaries are supported but the QM/MM interaction is truncated at a cut
off.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Mon Jun 11 2012 - 15:00:04 PDT
