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- PME, PBC, and pressure mdp settings for a 2D polarized MARTINI simulation
PME, PBC, and pressure mdp settings for a 2D polarized MARTINI simulation
- mboy@seas.upenn.edu
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3 years 6 months ago - 3 years 6 months ago #8717
by mboy@seas.upenn.edu
PME, PBC, and pressure mdp settings for a 2D polarized MARTINI simulation was created 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
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 6 months ago by mboy@seas.upenn.edu.
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3 years 6 months ago #8725
by vainikka
Replied by vainikka on topic PME, PBC, and pressure mdp settings for a 2D polarized MARTINI simulation
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.
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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- mboy@seas.upenn.edu
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3 years 5 months ago #8746
by mboy@seas.upenn.edu
Replied by mboy@seas.upenn.edu on topic PME, PBC, and pressure mdp settings for a 2D polarized MARTINI simulation
Thanks for the suggestion! I'll check it out! Sorry for the late reply!
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