On Mon, Feb 22, 2016, David Case wrote:
> On Mon, Feb 22, 2016, Ulf Ryde wrote:
>
> > Is there any possibility to simulate in Amber with a potential that is a
> > mixture of pure MM and QM/MM (i.e. of the type
> > E = (1-k) E_MM + k E_QM/MM
> >
> > include high-level QM in free-energy predictions with a MM reference
> > potential and a minimum of QM calculations.
Sorry: I missed the reference to a "minimum of QM calculations".
The TI procedure I described earlier seems to fit your first question, but
it requires that one carry out a QM calculation at every step of the TI
procedure. Whether you can afford to do this depends upon how expensive the
QM is, how big the difference between the MM and QM energy surfaces is, and
how much patience you have.
In principle, sander can do EVB calculations (and hence one could approach the
iterative fits described in the JPCB paper you cite); then a mixed potential
like that described above (and in my earlier email) could be used.
In practice, both the EVB codes and the TI codes in sander use "multisander"
and groups, and I'm not sure that one could combine the two in a single run
without making some code modifications.
Your best bet is to get a really accurate QM method that is also really fast.
I'll leave that as an exercise.
...dac
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Received on Mon Feb 22 2016 - 12:30:06 PST
