Re: AMBER: Fwd: QM region + cutoff larger that box

From: M. L. Dodson <>
Date: Mon, 06 Aug 2007 07:58:56 -0500

Francesco Pietra wrote:

> Hi Gustavo and Bud:

> Yes, as you suspected, the run that failed had qmmask ='1-2'
> while there was just one residue (initially I attached the out
> file, where the input file could be seen). When qmmask is set
> correctly, even this run went to completion up to tried 100ps.
> The far more serious problem is how to run the QM part, i.e.
> (1) which theory for the given problem,
> (2) what to look at (ESCF, EPtot, ..) to compare the potential
> energies of the conformers.
> Semiempirical PM3 AM1 MNDO are known to be unable to reproduce
> conformational energy differences between conformers. PM3, for
> example, gives for methylcyclohexane eq/ax 1.0-1.1, against the
> experimental (non-hydroxylic solvents r.t., 1.8). I am
> unfamiliar with PDDG or CARBI variants, though probably they
> follow the trend of their precursors: where one performs better,
> the other one fails. The trend being unpredictable.
> On the other hand, DFT-MM as in Amber9 can't deal with the
> medium effect, which is just my interest. Also, DFT requires
> very modern functionals and high basis sets to work with my
> cases.
> I am now exploring the performance of semiempirical QM-MM with
> test cases that embody features of the molecules of my
> interest. The conformational ratios for these test cases are
> known in condensed phase. I can't see how to approach the case
> better for the time being.
> Cheers
> francesco pietra

I have been using DFTB/SCC-DFTB with or without the dispersion
corrections (read the papers). This has the reputation of being
very good for QM treatment of chemical reactions in enzyme active
sites. This is not very different in concept from your interests
in solvent effects. Are you sure this is an inadequate method?
This approach is fairly different from DFT calculations in, e.g.,
Gaussian. I'm sure others can offer their impressions as well.

In my understanding, the dispersion corrections to DFTB/SCC-DFTB
are used to apply corrections for Van der Waals interacting
systems such as nucleic acids base pair stacking computations.

The energy of the system needs to be calculated by averaging over
an ensemble of structures as is always true for MD. The ensemble
is sampled by the dynamics, so the runs have to be "long enough"
to adequately sample the ensembles. How long is "long enough"
could serve as the definition of a "hard problem".

Good luck,
Bud Dodson

> --- Gustavo Seabra <> wrote:
>> Hi Francesco,
>> It's really hard to pinpoint the problem without more details. But what this
>> message is telling you, in general, is that your QM region is "expanding"
>> too far. QM atoms share one big pair list, and are not allowed to interact
>> with their periodic images. So, the QM region + cutoff must be kept smaller
>> than the box size.
>> (See a brief explanation in J. Phys. Chem. A 2007, 111, 5655-5664. A more
>> detailed explanation will be in an upcoming article)
>> This could be, as was suggested, one solvent molecule mistakenly included in
>> the QM region and that is diffusing away. It also did happen to me before
>> that, as the QM region moves, it assumes an extended position and suddenly
>> it's too large. Or, depending on the problem, you molecule could even
>> dissociate and then the parts separate too much.
>> Just to clarify one point, the QM region is recentered at every MD step, so
>> you don't have to worry about it diffusing out of the box, as long as it is
>> in one piece.
>> HTH,
>> Gustavo.
>>> -----Original Message-----
>>> From:
>>> [] On Behalf Of Francesco Pietra
>>> Sent: Saturday, August 04, 2007 4:33 AM
>>> To: Amber
>>> Subject: AMBER: Fwd: QM region + cutoff larger that box
>>> Although I suspected the problem does not arise from the box
>>> size, I have rerun md for the eq conformer. I started from
>>> prepin used successfully for the ax conformer in chcl3 and
>>> for both conformers in h2o. Setting the chloroform box 20A
>>> and md nstlim = 20,000.
>>> I have reexamined the and, they seem to be correct.
>>> It bombed at step 19150 with same indication "QM part +
>>> cutoff larger than box". As on previous runs, the mdcrd file
>>> shows the solute correctly immersed in molecules, allegedly
>>> chloroform. Say "allegedly" because of what said previously (below).
>>> Thanks
>>> francesco pietra
>>> --- Francesco Pietra <> wrote:
>>>> Date: Fri, 3 Aug 2007 10:02:35 -0700 (PDT)
>>>> From: Francesco Pietra <>
>>>> Subject: QM region + cutoff larger that box
>>>> To: Amber <>
>>>> QM-MM run successfully (20,000 steps) for axial
>>> methylcyclohexane in
>>>> chloroform along the lines of Tutorial A2 with Amber9.
>>>> Equatorial methylcyclohexane also run successfully for
>>> 10,000 steps.
>>>> When I attemped to double nstlim (20,000), run bombed because QM
>>>> region + cutoff
>>>> (8.0)
>>>> larger than box (15.0). I repeated the run, instead of two
>>> consecutive
>>>> 10,000 steps, just a single run of 20,000 starting from where the
>>>> 10,000-step run had been successful. Same error bombing.
>>> out file for
>>>> the latter run attached. I can't grasp where my error is.
>>>> An additional query: I was unable to delete chloroform from VMD.
>>>> Curiously, if I indicate to show carbon only, this is shown
>>> correctly
>>>> for the methylcyclohexane molecule, while chloroform is shown as an
>>>> ammonia-like umbrella with four identical atoms. I.e., chlorine is
>>>> shown as if it were carbon. Should I select a color for chlorine? I
>>>> was unable to trace where to deal with chlorine atom. I used the
>>>> chloroform box in Amber9.
>>>> All that because I am checking convergence for ESCF with a simple
>>>> test, flexible molecule.
>>>> Thanks
>>>> francesco pietra

M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-five_63-386_one
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Aug 08 2007 - 06:07:20 PDT
Custom Search