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 Tue Feb 27 2018 - 19:30:03 PST
