Re: AMBER: Fully QM periodic runs

From: Wei Zhang <>
Date: Wed, 14 Jun 2006 09:58:51 -0700

Hi Ross,

I also have this question. There is a parameter "qmcut" in "qmmm"
namelist, I tried to
reduce its value before and I do get a smaller quantum region, Is it
possible to get
a full quantum molecule by simply set "qmcut" to zero?



Ross Walker wrote:

>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 |
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>be read every day, and should not be used for urgent or sensitive issues.
>>-----Original Message-----
>>[] On Behalf Of Steven Winfield
>>Sent: Wednesday, June 14, 2006 09:04
>>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,
>>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?)
>>Steve Winfield.
>>The AMBER Mail Reflector
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Received on Sun Jun 18 2006 - 06:07:09 PDT
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