Re: How to qm/mm calculations with NAMD-QChem

From: RonitS Chem (
Date: Mon May 02 2022 - 17:48:06 CDT

Hello Marcelo,

Thank you for the detailed explanation. I assumed my system was
sufficiently equilibrated but I will do as you suggest. The issue is that
the simulation crashes with a segfault at that exact step every single
time, regardless of the starting configuration. The lack of error messages
in either NAMD or QChem also made pinpointing the issue difficult. Since
running the calculation with a semi-empirical method is not an option for
my project, I will try the following things and let you know,

1. Modify PC selection with stride and explicit PC file - I assume the
positions of the PC atoms will be updated and I don't have to provide a new
file at every timestep.
2. Equilibrate my system for a longer time before starting the qmmm step.

Related question, is there a debug or verbose option in NAMD, where I can
get more information about what is going on? I looked around found the
"++debug" option but that doesn't seem to print additional info. Please
let me know.


On Mon, May 2, 2022 at 2:08 PM Marcelo C. R. Melo <> wrote:

> 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"), 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 <>
> 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 ( 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/", 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 <>
>> 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 <>
>>> 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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