[gmx-users] missing prepare-qmmm.py

[Benson Muite]

Thanks.

On 7/10/19 2:38 PM, Dhr. D.W. Sjoerdsma (d.w.sjoerdsma) wrote:

> Dear Benson,
> Thank you for all the time you put in!
> I'll try one of these guys and share the updates!
> Sincerely,
> Derk Sjoerdsma
>
> On July 10, 2019 at 12:54 PM Benson Muite <benson_muite at emailplus.org> 
> wrote:
>>
>> 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>  <mailto: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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>