normal PME, PBC, and pressure mdp settings for a 2D polarized MARTINI simulation

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3 years 9 months ago - 3 years 9 months ago #8717 by mboy@seas.upenn.edu
Hello,

I'm attempting to simulate a charged system of polyelectrolytes grafted to a substrate. The system is effectively 2D, with a substrate, polyelectrolytes, and solvent on top of the substrate. I am setting up the box following the paper below, but this system contains no charge.

pubs.acs.org/doi/10.1021/ma201980k

I'm using polarized martini with PME. I'm not sure what the best PBC, PME, and pressure coupling settings would be for a martini version of my charged system.

Can anyone point me to a resource of people doing martini simulations with electrostatic interactions in a 2D setting, or provide some suggestions?

Thanks in advance for any recommendations. Any help or input is very welcomed.

Thanks,
Mike
Last edit: 3 years 9 months ago by mboy@seas.upenn.edu.

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3 years 9 months ago #8725 by vainikka
Hi,

Have you already read this one?

pubs.acs.org/doi/abs/10.1021/jp402615p

Might not be exactly what you need, but should help you in the right direction.

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3 years 8 months ago #8746 by mboy@seas.upenn.edu
Thanks for the suggestion! I'll check it out! Sorry for the late reply!

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