Hi Dan,
In principle there should not be problems with large separations between molecules in the QM region. But Qiantao is right, if either of the two molecules (chloromethane or acetonitrile) is alone in the QM region the SCF converges quickly and the forces look OK. Also, if you choose to put an acetonitrile in the vicinity of the chloromethane into the QM region (e.g. qmmask=':1,271'), everything looks good.
It is not a problem with PM6 parameters, MNDO/d shows the same problem. However, PM3 seems to behave well. So it might be related to the presence of d orbitals.
What really happens is that the SCF converges to a wrong state in the first step. This gives very bad forces as a result of which nasty things happen (see also the vlimit error) and with a bad structure in the second step, the SCF fails to converge. As to why the SCF converges to a wrong state in the first step for your example, I do not have an answer.
All the best,
Andy
On Jul 27, 2012, at 10:31 AM, Qiantao Wang wrote:
> Hi Dan,
>
> I noticed your QM region includes two far apart (~10 Angstrom) molecules
> (chloromethane and acetonitrile). This, from my experience, may cause
> problems sometime (I haven't investigated much about this issue; other QM
> developers may know more). Is there particular reason for you to do this?
> Otherwise, if you include chloromethane only, there should not be any
> problem, at least in my test run.
>
> Best,
> Qiantao
>
> On Wed, Jul 25, 2012 at 2:31 PM, <DJH71.pitt.edu> wrote:
>
>> Hi all,
>>
>> I was having problems running PM6 on a system that contained chlorine
>> atoms. I decided to experiment with a much simpler system: methane v.
>> chloromethane. My original system was solvated in acetonitrile and water,
>> so for consistency I solvated the methane and chloromethane as well. After
>> taking the same steps to equilibrate the solvated methane and
>> chloromethane, when methane was treated quantum mechanically with PM6, the
>> simulations ran without problems. When chloromethane was treated with QM,
>> the simulations immediately gave SCF convergence errors. I suspect it's an
>> issue with the d-orbital parameters, but that is speculation. A more
>> conclusive test might be to try fluoromethane as well.
>>
>> I've attached all input, output, prmtop and restart files for the two step
>> equilibration as well as the input and output files for the QM dynamics.
>> The files are in a tar-ed folder 'chloromethane.tar.gz'.
>>
>> It's entirely possible that this error is due to a fault on my part, but I
>> thought it was worth pointing out for investigation
>>
>> Dan Hatfield
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>>
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--
Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Fri Jul 27 2012 - 20:30:02 PDT
