Hi,
In section 22.1.1, it is said "The input (mdin) and starting coordinate
files must be the same for the two groups.", which makes me thought that
one could not mix MM and QM/MM.
I have just tested it (pentadiene test), and having different mdin's
does not seem to be enforced. Thus, one can indeed mix MM and QM/MM
using TI.
Thanks,
Gerald.
On 02/22/2016 04:30 PM, David A 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
>> 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.
>
> This is already implemented--at least I think so, although I have never
> actually done it myself....
>
> In sander, thermodynamic integration is implemented by creating two prmtop
> files, one for lambda=0 (which would be for E_MM) and one for lambda=1 (which
> would be for E_QM_MM). Then the standard lambda variable is the "k" in the
> equation above.
>
> In practice, the two prmtop files themselves are actually identical, since
> turning QM/MM on or off is determined by the ifqnt flag in the mdin file.
> See section 22.1.1 in the Amber 2015 Reference Manual. Your groupfile
> would look like the one given there, except that prmtop.0 and prmtop.1
> could be the same file, but the two "mdin" file would be different, with
> mdin.0 setting ifqnt=0 and mdin.1 setting ifqnt=1. The mdin.1 file would
> also include the other qm/mm-related options that are relevant when ifqnt
> is set to 1. Everything else should proceed as described in Section
> 22.1.4.
>
> Maybe someone on the list with more direct experience can chime in here. But
> the sort of calculation you describe is *supposed* to be straightforward, and
> was one of the reasons that TI in sander was implemented in the way that it
> was.
>
> ....regards...dave
>
>
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--
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Prof. Gerald MONARD
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Boulevard des Aiguillettes B.P. 70239
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e-mail : Gerald.Monard.univ-lorraine.fr
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Received on Mon Feb 22 2016 - 08:00:08 PST
