Hi Senal,
have you looked into the packmol-memgen utility? This would allow you to
specify which and how many species you want to add to your system. In a
way, I'd say there is no optimal number of ions here, you can simulate a
system of any size. The membrane you built will determine the box x and y
dimensions, so the number of ions you add will just be reflected in the
thickness of the system. I'd start with making the box roughly cubic and
add ions based on the expected density of the ionic liquid. I dont think
anyone will be able to tell the right number of ions right away, this is
what the simulation is for, no?
Kind Regards,
Thomas
On Sat, Apr 22, 2023 at 4:41 AM Delwakkada Liyanage, Senal Dinuka via AMBER
<amber.ambermd.org> wrote:
> Dear AMBER Mailing List Members,
>
> I hope this email finds you well. I am currently working on simulating a
> POPC bilayer system solvated in an ionic liquid, and I am seeking guidance
> on determining the total number of ion pairs required to effectively
> saturate the simulation box.
>
> I have successfully created a 100 x 100 x 85 angstrom simulation box using
> CHARMM-GUI, which consists of 12911 water residues. The lipid bilayer
> occupies a segment of 100 x 100 x 40 angstroms within the box. However, as
> I do not have any experimental data on the nature of the ionic liquid, I am
> in need of assistance in calculating the optimal number of ionic liquid
> molecules needed to effectively pack the system.
>
> I would greatly appreciate any guidance or suggestions on how to determine
> the appropriate number of ion pairs required for my simulation. Thank you
> in advance for your expertise and assistance.
>
> Best regards,
> Senal Liyanage
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>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Mon Apr 24 2023 - 00:00:02 PDT
