Now I have tried DMSO system with PM6 in serial. It can run without
termination by previous d-orbital error, but after it begins to run, I see
the warning message:
QMMM: WARNING!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: Job will continue with unconverged SCF. Warning energies
QMMM: and forces for this step will not be accurate.
QMMM: E = -0.2942E+07 DeltaE = -0.1385E+04 DeltaP = 0.1311E+01
QMMM: Smallest DeltaE = -0.2096E+02 DeltaP = 0.5187E+00 Step = 235
When I run the same system with PM3, it's no problem. Also I tried water
system, PM6 works well.
So anyone knows if PM6 works for system that contains DMSO? Thanks.
On Thu, May 2, 2013 at 7:34 PM, me, Nancy <bwan0408.gmail.com> wrote:
> Thanks, that was my question. The parallel speeds up the MM calculations
> even though it is not parallelized well for QM. PM3 works well in
> parallel. It just cannot run with PM6.
>
>
> On Thu, May 2, 2013 at 6:25 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Thu, May 2, 2013 at 5:48 PM, me, Nancy <bwan0408.gmail.com> wrote:
>>
>> > When I run QMMM simulation for DMSO system using PM6 in AMBER 12, I got
>> the
>> > error message "using d orbitals but the d orbital code is not
>> parallelized,
>> > please run in serial".
>> >
>> > I am wondering if there is any solution now for the problem? Thanks.
>> >
>>
>> If your real question is whether or not PM6 runs in parallel now, I think
>> the answer is no. Of course the `solution' to the problem causing this
>> error message is to run in serial (as indicated).
>>
>> Semi-empirical QM does not parallelize particularly well, anyway (due to
>> the fact that the diagonalization of the Fock matrix is rate-determining
>> and not easily parallelized). So even if/when it is parallelized, I would
>> not expect impressive speedups.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri May 03 2013 - 18:30:02 PDT
