[gmx-users] solvent evaporation modeling

Tue Dec 3 22:36:07 CET 2019

 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
>>>>>
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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
>
>
>
>
>
>
>
>