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Martini 3: to use PME or reaction-field
- nanogod
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2 years 1 month ago #9340
by nanogod
Martini 3: to use PME or reaction-field was created 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
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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