unanswered Martini 3: to use PME or reaction-field

  • nanogod
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2 years 3 months ago #9340 by nanogod
Hi all,

i noticed that ionic interactions are rather weak with Martini 3 compared to Martini 2 polarized model.

I did a simple test with 2 oppositely charged peptides and ran a simulation with reaction-field (epsilon_r 15) and one with PME (epsilon_r 2.5 and non polarized water), both martini 3. The difference is night and day. In the PME version the molecules got attracted right away and remained attracted. With reaction-field only few contacts were made.

is it sensible to use PME with martini 3? I have read about it in literature. maybe it was a mistake to use non polarized water. instead epsilon_r should have remained 15?

thank for the help :)

BR Morten

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