AMBER Archive (2006)

Subject: Re: AMBER: Fully QM periodic runs

From: Ken Merz (
Date: Thu Jun 15 2006 - 09:10:13 CDT

  This is not enabled in AMBER 9, but semiempirical QM MD on water
boxes has been done before by Gerald Monard's (see attached link to
the publication) and our research teams. He might be willing to share
the code if you contact him directly. Good luck. Kennie

On Jun 14, 2006, at 12:03 PM, Steven Winfield wrote:

> 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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Professor Kenneth M. Merz, Jr.
Department of Chemistry
Quantum Theory Project
2328 New Physics Building
PO Box 118435
University of Florida
Gainesville, Florida 32611-8435


Phone: 352-392-6973
FAX: 352-392-8722
Cell: 814-360-0376

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