From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Mon May 02 2022 - 16:08:22 CDT
Hi Ronit,
1. The default behaviour is to constantly update the point charges so as to
give the QM calculation a precise picture of the environment of the QM
region during the MD simulation. You can control how often this point
charge update occurs, if you determine that the selection should not change
often. This can be done with the keyword "qmPCStride".
If you do not want any update at all, and instead want to define point
charges yourself using a separate PDB file, you can use the keyword
"qmCustomPCSelection". Please check the documentation for the keywords in
either case.
2. I usually make the script executable (in linux, that would mean
"chmod +x script.py"), so that it can be called and executed
directly, without the "python" call. But if you have it working like this
(as your output suggests) I would not change it.
>From your first email, it seems that you have a QMMM simulation crashing
early and often. The most common source of this problem is an unstable
system. QM calculations are extremely fragile, so "unstable" here could
mean one or two atoms moving a little too fast, and preventing the QM
package from converging after only a few MD steps. The solution is usually
to further equilibrate the system with classical MD before switching QM/MM
on, or running a QMMM equilibration with a semi empirical (more forgiving)
method.
Let me know how that goes!
Best,
Marcelo
On Mon, May 2, 2022 at 12:24 AM RonitS Chem <ronits.chem95_at_gmail.com> wrote:
> Hello,
>
> I sincerely apologize since the previous email got cut off before I could
> explain the issue. I have attached the NAMD output file (test.out), the
> QChem output file (qmmm.in.out) and the qmmm_0.input.result file. There is
> no qmmm_0.input.TmpOut generated. As I was saying in my previous email,
> in the portion that got cut off, I have a few questions about the
> implementation,
>
> 1. In the NAMD output file I print the number of QM atoms (numQMatms) and
> the number of point charges (numPntChr) and the latter seems to vary in
> different QChem calls. How are the point charges selected?
> 2. In the qmExecPath keyword I have "python /path/to/run_qchem.py", is
> that the correct way to set up this type of calculation since qmSoftware is
> custom?
>
> Please let me know if you require any further information. Thank you
> for your help.
>
> Best,
> Ronit
>
> On Sun, May 1, 2022 at 8:50 PM Marcelo C. R. Melo <melomcr_at_gmail.com>
> wrote:
>
>> Hi Ronit,
>>
>> From your email it is hard to tell what could be going on.
>> Can you share the output files from NAMD and from QChem itself (
>> qmmm_0.input.TmpOut)?
>>
>> Best,
>> Marcelo
>>
>> On Sun, May 1, 2022 at 7:07 PM RonitS Chem <ronits.chem95_at_gmail.com>
>> wrote:
>>
>>> Hello all,
>>>
>>> I was trying to run qm/mm calculations using the NAMD-QChem with the
>>> python
>>> wrapper provided. However, NAMD crashes at the exact same step everytime
>>> I
>>> try to run any calculation. The step is as described below, taken
>>> directly
>>> from the output file but redacted for brevity,
>>>
>>> TCL: Running for 2000000 steps
>>>
>>> Info: List of ranks running QM simulations: 0.
>>>
>>> You are running Q-Chem version: 5.4.2
>>>
>>> #
>>>
>>> # job setting
>>>
>>> # .
>>>
>>> # .
>>>
>>> # qchem directory setting
>>>
>>> # .
>>>
>>> # .
>>>
>>> # parallel setting
>>>
>>> # .
>>>
>>> numQMatms: 7 ; numPntChr 1488
>>>
>>> Sum of the charges: -1.7763568394002505e-15
>>>
>>> command: cd
>>>
>>
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