Hi,
This is indeed an important feature request that some of us have already
thought of, but not yet implemented...
As far as I know, only the SEBOMD part (pure semiempirical QM, no QM/MM)
has a lambda term to mix between full QM and MM representations.
In details, I am not sure that it is very easy to implement because the
way the QM/MM has been implemented in sander (i.e., it was not designed
at the first place to do such thing). Multisander could do the trick I
guess.
However, for a possible fast workaround, you could check the sander API
and work with two instances of the same system and then mix them the way
you desire.
Best regards,
Gerald.
On 02/22/2016 03:56 PM, Ulf Ryde wrote:
> Dear all,
> 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
> where k is an adjustable parameter (like lambda in standard free-energy perturbations),
> so that you can do free-energy perturbations along this parameter, going from MM to QM/MM.
> Such a potential is employed in Warshel's paradynamics approach (J Phys Chem B 115 (2011) 7950), which is one of the most promising ways to include high-level QM in free-energy predictions with a MM reference potential and a minimum of QM calculations.
>
> I do not find such an approach in the manual, but I suppose it is simple to implement for somebody acquainted with with the QM/MM code.
> Can somebody help us with such an implementation or suggest how it should be done?
>
> Best Regards,
> Ulf
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>
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Received on Mon Feb 22 2016 - 07:30:06 PST
