[gmx-users] solvent evaporation modeling

SAKO MIRZAIE sako.biochem at gmail.com
Mon Dec 9 21:24:57 CET 2019 

Dear Anders and Kalil,

Thank you for your answers and for sharing the scripts. I will help a lot.

Best,


On Tue, Dec 3, 2019 at 5:12 PM Anders Støttrup Larsen <anders.sl at gmail.com>
wrote:

> Hi Sako
>
> I did something similar where I dehydrated a system of water molecules, in
> my case a crystal but the principles are the same.
>
> I have uploaded the script at
>
> https://github.com/aslarsen/gromacs_dehydration/blob/master/gromacs_dehydration_MPI_V2.py
>
> It was used in this paper
> https://pubs.acs.org/doi/abs/10.1021/acs.cgd.7b00889
>
> I used gromacs 5.1.4 so you might have to update it to your version and
> set whatever parameters you want.
>
> Best Wishes
> Anders
>
> On Tue, Dec 3, 2019 at 10:36 PM Kalil Bernardino <
> kalil.bernardino at gmail.com> wrote:
>
>>  Dear Sako,
>>
>>
>> Unfortunately I don't have access to the script in the present since I'm
>> in
>> the middle of a travel. But anyway it was done in a specific way for the
>> system that we were working on that time and would need some changes to
>> work with different systems.
>>
>> I can describe to you the general idea here.
>>
>>
>> First, there is two ways to simulate the solvent evaporation and we
>> performed both in the paper André cited. The more physical way, since we
>> were working with a liquid vacuum interface, suppose perpendicular to z
>> direction, was to run a short simulation, save the final structure, check
>> which molecules are above some zcut value, exclude they from your
>> structure, rewrite the topology file to update the number of molecules,
>> run
>> the grompp to produce the new tpr and run a new short simulation. This
>> would be something similar to have a liquid with a vacuum pump at z =
>> zcut,
>> and any molecule that enters the vacuum pump will be removed from the
>> system. For this protocol, you should work with constant volume
>> simulations.
>>
>>
>> The problem with this procedure is that it can be very slow, specially
>> when
>> you have too few solvent remaining or if your system have a small vapor
>> pressure, as is your case since you are working with water. So, if you
>> want
>> to complete dry your system, you can remove molecules randomly in the
>> following way. You may or may not want to create a liquid/vacuum
>> interface,
>> depending if you want to simulate the molecule in some interface or if you
>> want to simulate the bulk of something that in being dried. If you have a
>> vacuum interface, you need to work with NVT simulations, but in order to
>> make a bulk simulation you should do in a NPT ensemble.
>>
>>
>> 1- Equilibrate your system with the solvent
>>
>> 2- Save the final structure
>>
>> 3- Delete some fraction of randomly selected solvent molecules. You can do
>> this directly with some script or can use the gromacs command genion to
>> randomly convert some molecules in some monoatomic specie (for instance,
>> "genion -np 60 -pname DEL" and select the water for replace 60 water
>> molecules with 60 particles with name DEL), make_ndx to generate a index
>> file with a group including every molecules except the specie produced by
>> genion (DEL in the example) and then the editconf reading the index.ndx in
>> order to produce a new .gro file with every molecule except the deleted
>> ones. This .gro will be your initial structure for next step. If you want
>> to use the gromacs commands for this remotion, remember to run the grompp
>> again from your final structure to produce a new tpr file before using
>> genion.
>>
>> 4- Rewrite your topology file in order to update the number of solvent
>> molecules
>>
>> 5- Run grompp and mdrun to do a short simulation with this small numer of
>> water molecules and save the final structure
>>
>> 6- If still have water in your system (or if have more water than you want
>> in your final structure), go back to step 3 and continue removing.
>>
>>
>> You should not remove a large amount of molecules in a single step or this
>> can lead to some artificial structures. And by the end of your process,
>> when you have only a small amount of solvent, I think it is better to
>> reduce even more the amount removed at each step (which is not so bad
>> because your simulation will run faster at this point).
>>
>>
>> Hope this protocol helps you.
>>
>>
>> Best,
>>
>> Kalil
>>
>>
>>
>> Em seg., 2 de dez. de 2019 às 14:14, SAKO MIRZAIE <sako.biochem at gmail.com
>> >
>> escreveu:
>>
>> > 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
>> >>>>>
>> >>>>> * Please search the archive at
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>> >>>>> posting!
>> >>>>>
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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
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> --
>> Gromacs Users mailing list
>>
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>
>

-- 
***********************************************
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/

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