normal Martini Dielectric Constant Question

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5 years 2 months ago #7995 by nlogn
Hi all,

I'm not sure I understand how to set the relative dielectric constant, when dealing w/ charged bead type interactions in Martini. Should I be setting it's value to 15 regardless of the dielectric constant/level of charge screening going on in the corresponding system? If so, is there some justification for this choice - or any differences in how the dielectric constant is treated between Martini V. 2.2 & 3.0?

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5 years 2 months ago #8006 by bart
Replied by bart on topic Martini Dielectric Constant Question
The Martini FF has been parametrized towards dielectric screening constant of 15, part of the electrostatic interactions have been included in the LJ parameters, therefore changing the screening constant would mean that you would also have to parametrize the LJ interactions. In short we would not advice fiddling with the screening.

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4 years 7 months ago #8216 by bond_007
Replied by bond_007 on topic Martini Dielectric Constant Question
Hi,
I had a couple of similar questions regarding the dielectric constant in MARTINI -
1) Do we have to explicitly specify the dielectric constant in the .mdp file in gromacs by setting the epsilon_r option? Or is it already taken care of in some other way(implicitly) in MARTINI?

2) How does the dielectric constant change when implementing a Reaction Field method? i.e. (epsilon_r and epsilon_rf parameters)

3) Could you provide some background reasoning about how the dielectric value is set to 15?

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4 years 7 months ago #8221 by bart
Replied by bart on topic Martini Dielectric Constant Question
Take a look at the default input mdp on our webpage.

cgmartini.nl/images/parameters/exampleMD...tini_v2.x_new-rf.mdp

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4 years 7 months ago #8223 by bond_007
Replied by bond_007 on topic Martini Dielectric Constant Question
Thanks bart! I just wanted to confirm that the epsilon_r parameter has to be explicitly specified as 15 for MARTINI runs and is not the default.

Also, a follow-up to your previous post. You said that the dielectric should not be changed since part of the electrostatic interactions were included in LJ parameters. Could you please expand on this?

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4 years 7 months ago #8225 by xavier
Replied by xavier on topic Martini Dielectric Constant Question
Hi,

1) Do we have to explicitly specify the dielectric constant in the .mdp file in gromacs by setting the epsilon_r option? Or is it already taken care of in some other way(implicitly) in MARTINI?

answer: the value for epsilon_r has to be explicitly given in the mdp file. As shown in the mdp files indicated by Bart.

2) How does the dielectric constant change when implementing a Reaction Field method? i.e. (epsilon_r and epsilon_rf parameters)

answer: See value in the mdp file indeed. To be honest Iam not sure what the point of a RF if the epsilon_rf is zero! I have never noticed that.

3) Could you provide some background reasoning about how the dielectric value is set to 15?

answer: the value of 15 comes with a long history that you'll have to has master Marrink to get the details. I just realized that the value was 20 early on as described in (J. Phys. Chem. B, Vol. 108, No. 2, 2004). The screening of the electrostatic interaction of the lipid heads groups to reproduce bilayer properties was most likely an important test.

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4 years 7 months ago #8226 by bond_007
Replied by bond_007 on topic Martini Dielectric Constant Question
Thanks for inputs!

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