Hi Ross
Thanks for your response. The junk in my input file is evolutionary
leftovers from previous runs. I used a small system and a small cutoff
because I'm trying to hone in on the problem. I have done several dozens
of picoseconds of qmmm with this system, gradually ramping up from 0K to
16K at constant pressure. So I don't think that the evolutionary
leftovers in the input file are causing the problem.
I want to draw your attention to the following:
According to the attached output file (and the qm_region.pdb file), the
min and max Z are -5.884 and 5.884, which gives a size of 11.76. So the z
size + 2*cutoff is 19.76Ang. But then later in the same output file, it
says the QM Z size is 29.962Ang. Isn't this a conflict? The system only
moved one step. I set it up this way to hone in on the problem.
Andrew
> Hi Andrew,
>
> The bounds for QMMM calculations are slightly different than the bounds
> for
> regular MM calculations. The MM pairlist is separate for each atom. Thus
> with an 8A cutoff each atom is surrounded by a sphere of 8 angstroms
> radius
> which should not extend across two boxes. For the QM region, for stability
> reasons since having different charges in the Fock matrix for different QM
> atoms can cause problems, each atom shares the same non-bond list. Thus
> each
> QM atom interacts with MM atoms that are within qmcut of ANY QM atom. This
> means that your QM region is effectively surrounded by a MM region of size
> QMcut. In order to not violate the minimum image convention this means
> that
> your box must be at least the largest dimension of the QM region + the
> cutoff.
>
> This should be what the message below is telling you. Your box can contain
> a
> sphere of 11.146 angstroms radius But the QM dimensions plus the cutoff
> are
> larger than this. Solution = use a much larger water box.
>
> With regards to the difference in the absolute values of the bounding box:
>
> ERROR: QM region + cutoff larger than box dimension:
> QM-MM Cutoff = 4.0000
> Coord Lower Upper Size Radius of largest sphere inside unit
> cell
> X -5.632 13.150 18.782 11.146
> Y -5.431 13.671 19.102 11.146
> Z -15.168 14.794 29.962 11.146
>
> One needs to consider the coordinates to simply be relative here. For
> simplicity inside the QM routines the QM region is extracted from the
> main,
> unimaged, coordinate array. It is then imaged and centered. Then the MM
> atoms that fall within the cutoff are also rebased to be within the QM
> calculations central QM region origin setup. Hence the coordinates written
> from within the QM region will not have the same origin as the inpcrd
> file.
>
> Note, looking at your system:
>
> 1) NATOM = 1280
>
> This is VERY small, especially since you have some 160 QM atoms. Likely
> you
> have nowhere near enough water.
>
> 2) cut=4.0
>
> I assume you just made this smaller in order to see if you could get the
> calculation to run, rather than actually intending to run simulations with
> a
> 4 angstrom cutoff. This should NEVER be reduced below 8.0. In fact I vouch
> that the sander code be modified to refuse to run with cutoffs of less
> than
> 8.0.
>
> 3) Your mdin file appears to be full of lots of junk and strange settings.
>
> imin=0, maxcyc =1000,
>
> You specify maxcyc even though imin=0. This just leads to confusion.
> You set tempi=1.0 even though you have irest=1. Again just confusion.
> You specify tautp=0.1 even though you have ntt=3 which does not use tautp.
> temp0=16.0 = You really want to run at just 16K? Scaling from 14 kelvin to
> 16 kelvin over 2000 steps?
> You try to do NTP (ntb=2,ntp=1) at VERY low temperature. Use of constant
> pressure at low temperatures will undoubtedly lead to instabilities.
> You set offset=0.09 but are running PME. Again confusing.
> You set clambda even though you are not running thermodynamic integration.
>
> Good luck,
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> 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-----
>> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
>> Behalf Of aapeters.ncsu.edu
>> Sent: Tuesday, April 20, 2010 9:36 AM
>> To: amber.ambermd.org
>> Subject: [AMBER] QM/MM cut problem
>>
>> Hello users
>>
>> When using Amber10 QM/MM I get errors complaining my box is too small.
>>
>> But when I look at the structure and at the QM region coordinates,
>> there
>> seems to be enough space. There seems to be a conflict between the
>> coordinate extremes written out in the first part of the output file
>> (or
>> the qmmm_region.pdb file), and the bounds written out in the latter
>> part
>> of the output file:
>>
>> ERROR: QM region + cutoff larger than box dimension:
>> QM-MM Cutoff = 4.0000
>> Coord Lower Upper Size Radius of largest sphere inside
>> unit
>> cell
>> X -5.632 13.150 18.782 11.146
>> Y -5.431 13.671 19.102 11.146
>> Z -15.168 14.794 29.962 11.146
>>
>> To hone in on the problem, I set up a run that crashes on the second
>> step.
>> So
>> 1) the initial qm region positions are written in the output file
>> 2) the system takes one step, and writes "qmmm_region.pdb", the
>> corresponding pdb file
>> 3) the system crashes on the 2nd step, writing the bounds violation in
>> the
>> output file.
>>
>> Assuming positions barely change in one step, there seems to be a
>> significant conflict within the code about where it thinks the bounds
>> are?
>>
>> I attached the output files
>>
>> Thanks in advance for any help.
>>
>> Andrew Petersen
>
>
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Received on Tue Apr 20 2010 - 11:30:04 PDT
