[gmx-users] missing prepare-qmmm.py

[Benson Muite]

Dear Derk,

Ok. Got the same result. Perhaps contact one of the main authors of the 
following papers:

Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC by 
Viacheslav Bolnykh et al

https://doi.org/10.26434/chemrxiv.8067527.v1

MiMiC: A Novel Framework for Multiscale Modeling in Computational 
Chemistry by Jógvan Magnus et al

https://doi.org/10.26434/chemrxiv.7635986.v1

If you make progress, please update the list so that the documentation 
can be updated.

Regards,

Benson

On 7/10/19 1:25 PM, Dhr. D.W. Sjoerdsma (d.w.sjoerdsma) wrote:
> Dear Benson,
>
> Thank you for your reply :)
> I indeed set the -DCMAKE_PREFIX_PATH flag correctly. I also looked what the
> syntax of the  -DCMAKE_INSTALL_PREFIX was.
> However after trying the correct syntax, I still was not able to get the
> prepare-QMMM.py
>
> It should however be generated as is said in the text: " After preparing the
> input for GROMACS and having obtained the preprocessed topology file, simply run
> the Python preprocessor script provided within the MiMiC distribution to obtain
> MiMiC-related part of the CPMD input file. "
> -http://manual.gromacs.org/documentation/2019-rc1/reference-manual/special/mimic-qmmm.html
>
> I also tried checking the src's, but I didn't got any luckier there..
>
> Sincerely,
> Derk
>
>
> On July 1, 2019 at 7:10 PM Benson Muite <benson_muite at emailplus.org> wrote:
>> Hi,
>>
>> Was -DCMAKE_PREFIX_PATH set to the location at which CommLib library was
>> installed?
>>
>> Not sure if
>>
>> -DCMAKE_INSTALL_PREFIX:PATH=/home/derk/Prog/gmx19
>>
>> is a typo and should be
>>
>> -DCMAKE_INSTALL_PREFIX_PATH=/home/derk/Prog/gmx19
>>
>> prepare-qmmm.py
>>
>> does not seem to be in the sources at
>> https://gitlab.com/MiMiC-projects/CommLib and
>> https://github.com/gromacs/gromacs, though maybe automatically generated.
>>
>> Benson
>>
>> On 7/1/19 3:52 PM, Dhr. D.W. Sjoerdsma (d.w.sjoerdsma) wrote:
>>> Hello,
>>>
>>> After compiling GROMACS with the MiMiC option, I was not able to locate the
>>> prepare-qmmm.py file. I do not know whether this is a result of a faulty
>>> installation or if it is something else
>>>
>>> I used the following flags:
>>>
>>> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_DOUBLE=ON -DGMX_
>>> MIMIC =ON -DCMAKE_INSTALL_PREFIX:PATH=/home/derk/Prog/gmx19 -DGMX_MPI=ON
>>> -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
>>>
>>> Sincerely,
>>> Derk Sjoerdsma
>>>
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