[gmx-users] solvent evaporation modeling

[SAKO MIRZAIE]

Dear André,

Thank you very much for your email and hope Kalil has the script.

Best regards

On Mon, Dec 2, 2019 at 7:15 AM André Farias de Moura <moura at ufscar.br>
wrote:

> Dear Sako,
>
> I'm ccing Kalil, who actually wrote and run the script to remove solvent
> molecules, he might still have it.
>
> regards
>
> Andre
>
> On Mon, Dec 2, 2019 at 2:54 AM SAKO MIRZAIE <sako.biochem at gmail.com>
> wrote:
>
>> Dear André,
>>
>> Thank you for your response.
>> Could you send me such a script?
>>
>> On Sun, Dec 1, 2019 at 7:15 PM André Farias de Moura <moura at ufscar.br>
>> wrote:
>>
>>> Dear Sako,
>>>
>>> we did something like that a few years ago, please take a look at DOI 10.1039/C4CP03519D
>>> for details.
>>>
>>> in a nutshell: you need a script that runs a sequence of short
>>> equilibration and production runs after a number of solvent molecules are
>>> removed (implying that topology needs to be updated for the number of
>>> solvent molecules at each round, so the script needs to include some
>>> parsing of the files as well).
>>>
>>> Andre
>>>
>>> On Sun, Dec 1, 2019 at 8:03 PM SAKO MIRZAIE <sako.biochem at gmail.com>
>>> wrote:
>>>
>>>> Hi All,
>>>>
>>>> I want to simulate a polymer: protein system in a way that water solvent
>>>> will evaporated gradually. How should I do that? What parameters are
>>>> needed
>>>> to be included in the mdp file.
>>>>
>>>> Best
>>>>
>>>>
>>>>
>>>> --
>>>> ***********************************************
>>>> Sako
>>>> --
>>>> Gromacs Users mailing list
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>>>
>>>
>>> --
>>> _____________
>>>
>>> Prof. Dr. André Farias de Moura
>>> Department of Chemistry
>>> Federal University of São Carlos
>>> São Carlos - Brazil
>>> phone: +55-16-3351-8090
>>>
>>
>>
>> --
>> ***********************************************
>> Sako Mirzaie
>> Sako Mirzaie
>> Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad
>> University of Sanandaj, Sanandaj, Iran
>>
>> Visiting Professor, Advanced Pharmaceutics
>>
>> & Drug Delivery Laboratory
>>
>> Leslie Dan Faculty of Pharmacy
>>
>> University of Toronto
>>
>> 144 College Street, Toronto, Ontario
>>
>> Canada M5S 3M2
>>
>> http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en
>>
>> http://www.scopus.com/authid/detail.url?authorId=54886431500
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
>> https://www.researchgate.net/profile/Sako_Mirzaie/publications/
>>
>>
>>
>>
>>
>>
>>
>
> --
> _____________
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
>


-- 
***********************************************
Sako Mirzaie