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normal PME parameters: Based on "New" methodology

  • peter
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2 years 6 months ago #9184 by peter
PME parameters: Based on "New" methodology was created by peter
Hello everyone,

I could not find the general parameters for a PME simulation among the Example scripts . For my simulation, I would like to use polarizable water along with the PME electrostatics. However, I am not sure regarding the electrostatics parameters that I should use.

Based on this recent paper , I am considering the following electrostatics options. Could someone please let me know if they seem fine to start with?

coulombtype                = PME 
coulomb-modifier           = Potential-shift-verlet
rcoulomb                   = 1.1
epsilon-r                  = 2.5 ; with polarizable water
Thank you for reading my post!

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2 years 5 months ago #9207 by riccardo
Replied by riccardo on topic PME parameters: Based on "New" methodology
Those parameters look good to me. Plus, those authors in that paper seem like trustworthy people ;-)

It's would be probably a good idea to include a PME mdp among the default mdps, will try to remember to propose that...

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2 years 5 months ago #9211 by peter
Replied by peter on topic PME parameters: Based on "New" methodology
Thank you very much!
Although it seems the "coulomb-modifier" term is not necessary with PME.

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2 years 1 month ago - 2 years 1 month ago #9354 by nanogod
Replied by nanogod on topic PME parameters: Based on "New" methodology
There is a huge difference in electrostatic interaction depending on if you choose PME (very strong) or the tutorial mdp file (very inert interaction). I can’t seem to trust neither representation

Is the polarized Walter model at all included in Martini 3? I don’t see it
Last edit: 2 years 1 month ago by nanogod.

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2 years 1 month ago #9355 by riccardo
Replied by riccardo on topic PME parameters: Based on "New" methodology
No polarizable Martini 3 water model available yet.

[be sure to use the correct PME vs reaction-field settings (see, e.g. cgmartini.nl/index.php/component/kunena/...oom-temperature#9351 ).]

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2 years 1 month ago #9356 by nanogod
Replied by nanogod on topic PME parameters: Based on "New" methodology
Hi Riccardo,

Thanks for the quick reply. I have used martini 2 a lot but only just started to use Martini 3.

I do use epsilon_r=15. However I see a huge difference if I use PME vs reaction-field. I don’t really see in any of the turtorials that PME is used. In the martini 3 paper supplementary information I do see it mentioned though. I am afraid if I can trust the results atm and considering switching back to Martini 2 :(

BR
Morten

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2 years 1 month ago #9357 by riccardo
Replied by riccardo on topic PME parameters: Based on "New" methodology
Good that you are being careful, you should always validate your simulation results. How are you validating them? Experimental data / atomistic data? If there are no exp./atomistic data for your system, try to build a closely-related system for which there are reference data and see how Martini 3 results compare.

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