Jim,
The QM check works fine, this looks like a problem with qmmask: the QM selection gives 40 atoms in AAA_salt_qmmm_orc_David2.out while ambmask with the same mask selects only 6 atoms (for what I think is the matching prmtop/inpcrd that you sent in a different email). This makes the QM region plus cutoff too large to fit in the box. You can see this in the output, the QM region + cutoff size in x, y, and z direction must be smaller than two times the radius of largest sphere inside the unit cell.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Feb 27, 2018, at 7:26 PM, James Kress <jimkress_58.kressworks.org> wrote:
>
> David,
>
> Here are some test cases where I get the QM_CHECK_PERIODIC error. The MM cutoff is 8 as is the qm cutoff. In David4 qmcut = 1.0 and it still fails.
>
> Jim
>
> -----Original Message-----
> From: David A Case [mailto:david.case.rutgers.edu]
> Sent: Tuesday, February 27, 2018 8:50 PM
> To: jimkress_58.kressworks.org; AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error
>
> On Tue, Feb 27, 2018, James Kress wrote:
>>
>> From my reading of the user’s guide, solvent can be in the QM region,
>> it appears that this could be done using &vsolv. However, when I try
>> that I get the dreaded (and unresolved to the best of my knowledge)
>> “SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> QM region +
>> cutoff larger than box cannot continue, need larger box.” error.
>
> How big is your box? What is your qm cutoff (which is generally set to the cutoff used in MM, something like 8 or 9 Ang)? It looks to me like the code right before the QM_CHECK_PERIODIC error prints out quite a bit of information about what it's unhappy about: can you try to decode that, or post the full message?
>
> It's not clear (yet) that there is anything to "fix" in the periodic check code. Amber's QM/MM code is designed for a small and compact QM region, in the presence of a large amount of MM environment. "Small" and "large" in this context are determined by the code in qm_mm.F90 right around where the error message is triggered.
>
> ....dac
>
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Received on Wed Feb 28 2018 - 00:00:02 PST
