Re: AMBER: box size bomb in QMMM calculation

From: M. L. Dodson <>
Date: Wed, 13 Jun 2007 04:43:52 -0500

Ross Walker wrote:
> Hi Bud,
>>> cut off unreasonably small for this, say 0.1 A just to
>> force it to get to
>>> the pdb writing stage.
>> That was my plan, but it never gets far enough to do that. It bombs
>> before the QM region pdb write occurs.
> Did you try setting cut=0.1? That should get you through to the pdb writing
> phase, although obviously the actual MD will be garbage. Alternatively you
> could try turning off periodic boundaries - set ntb=0, then it will skip the
> cut off bounding check and you;ll get a pdb.
>> Unfortunately, I'm leaving tomorrow morning to go to the US
>> Grand Prix.
> Wow, lucky for some... I just have to resign myself to watching it on Speed.
> Enjoy...
> All the best
> Ross

I'll try that first thing when I get back.

I thought up another possibility: The restart file furnishing the
initial coordinates is not imaged, but my (still possibly bogus) water
selection procedure works on an imaged and centered system. The
identified close waters may have numerically large coordinates in the
unimaged restart file. If I start the simulation with the imaged and
centered restart file instead, I should be able to at least get far
enough along to generate a QMMM region pdb file. Alternatively, I could
do a single step of classical MD with iwrap=1 to get a restart file with
all coordinates in the primary cell.

In any case, I'm off to vacation for a week. Thanks for the help!

Bud Dodson

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Received on Sun Jun 17 2007 - 06:07:05 PDT
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