AMBER Archive (2008)

Subject: RE: AMBER: Fully QM periodic runs

Date: Mon Nov 24 2008 - 15:28:36 CST

Hi Ross,

We've recently become interested in performing periodic QM/MM calculations
in Amber, but with a purely QM system. We certainly appreciate that there
would be practical limitations with respect to the system size, but have
there been any developments in Amber 10 (or planned for Amber 11) that would
facilitate these kinds of calculations? Would it be feasible to make a small
change to the code to get this working, or would there be significant barriers
to this?

We would sincerely appreciate any guidance you can provide.

Best regards,
Steven Corcelli and Hannah Fox

Original message:

Hi Steven,
Unfortunately in Amber 9 one cannot do a pure QM periodic system. You can
only do QM/MM with periodic boundaries and this has the restriction that the
QM region dimension + cutoff must not extend beyond the box boundaries. I.e.
it is designed for modelling say an active site in a protein that is then
The implementation is also designed for relatively small QM systems of the
order of 200 atoms max. You can go larger than this using divide and conquer
but even them the time per step is prohibatively large to do MD with. Thus
periodic boundaries for pure QM systems is not very useful on this scale
since if you were to have say just a box of 200 waters and treat this
periodically I think you would see artifacts due to the enforcing of
periodicity on such small systems.
Such an option may be added to Amber 10 but there are no distinct plans at
All the best
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |
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be read every day, and should not be used for urgent or sensitive issues.

> -----Original Message-----
> From:
> [] On Behalf Of Steven Winfield
> Sent: Wednesday, June 14, 2006 09:04
> To:
> Subject: AMBER: Fully QM periodic runs
> Dear Amber users,
> I am trying to perform a QM/MM run on a box of water, treating
> everything quantum mechanically, but I'm running into some problems.
> If I use, for example, the TIP3PBOX unit as my input structure then
> sander fails because the size of the QM region is bigger than the
> periodic box. This is due to some atoms protruding out of the primary
> simulation cell. Even if I turn on iwrap=1 the problem is
> still present
> because the wrapping is done to the whole molecule only when
> the first
> atom of that molecule moves out of the primary cell. Also,
> introducing
> some vacuum around the structure still fails when molecules cross the
> new cell boundary.
> So my question is: Can a fully QM periodic run be done in the current
> AMBER, and if so how? (Wrapping atoms back into the primary cell
> individually rather than with the rest of the molecule for example?)
> Thanks,
> Steve Winfield.

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