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normal Use of Counterions

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11 years 2 months ago #1394 by anna_duncan
Use of Counterions was created by anna_duncan
I'm simulating a protein in a membrane using MARTINI, with a lipid that has a net negative charge. I am unclear as to whether I should definitely include counter ions to neutralise my system. Is there, for instance, any problem with their size making their inclusion 'less realistic' in a coarse-grained system? Or do the advantages far outweigh any potential drawbacks? Is it even a matter for debate or just totally obvious that I should be including counter ions?

I know that there exist MARTINI counter ions, however, use of counter ions is not touched upon in tutorials and in one of the 'example applications', 'KALP in a DPPC bilayer', they are not included, although in others they are ('HA fusion peptides', for example).

Many thanks,

Anna

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11 years 2 months ago #1395 by djurre
Replied by djurre on topic Use of Counterions
That is definitely a matter of debate:-)

Models for Ions in general (also atomistic) are problematic (=not very good). Because of that some people say you should better not include them. Others think it is better to have a not very good model for ions than not have them at all.

If you use ions you'd probably best use monovalent ions, those models are probably better then the divalent ones.

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  1. Force Fields
  3. Other Molecules
  5. Use of Counterions
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