Dear David and Gerald,
We have tested the approach on our systems and it seems to work smoothly and give reasonable results.
Thank you for your kind help.
Ulf
________________________________________
From: David A Case [david.case.rutgers.edu]
Sent: 22 February 2016 16:30
To: AMBER Mailing List
Subject: Re: [AMBER] Paradynamics with Amber
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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Received on Fri Feb 26 2016 - 08:30:03 PST
