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Add ions into the protein-lipids system
- thu nguyen
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11 years 3 months ago #1344
by thu nguyen
Add ions into the protein-lipids system was created by thu nguyen
Dear All,
I see in Example Applications, some files such as kalp_DPPC.top, gly_A_monomer_DPPC.top... don't include ions. But i see in their .itp files, the system has not zero charge. This is different with MD-AA (the system has neutralized with ions).
I want to know why. Thank so much for any idea !
Regards,
KT
I see in Example Applications, some files such as kalp_DPPC.top, gly_A_monomer_DPPC.top... don't include ions. But i see in their .itp files, the system has not zero charge. This is different with MD-AA (the system has neutralized with ions).
I want to know why. Thank so much for any idea !
Regards,
KT
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- kmcallenberg
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11 years 3 months ago #1346
by kmcallenberg
Replied by kmcallenberg on topic Add ions into the protein-lipids system
While extra ions added to generate a particular salt concentration is not recommended, system charge neutrality is definitely encouraged with MARTINI. I think you should just assume that the ions haven't been added yet in the two example applications that you referenced.
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- djurre
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11 years 3 months ago #1347
by djurre
Replied by djurre on topic Add ions into the protein-lipids system
Out of curiosity, what is the disadvantage of using a particular salt concentration?
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- kmcallenberg
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11 years 3 months ago #1348
by kmcallenberg
Replied by kmcallenberg on topic Add ions into the protein-lipids system
"Keeping in mind the difficulty of modeling of ions already with AA force fields, the CG ion force field is only qualitatively accurate." Marrink et al. J Phys Chem B 2007
I think there are other places that more explicitly discuss the use of a physiological salt concentration. There must be an explicit recommendation to only add enough ions to neutralize the system somewhere, because it's followed very widely.
I think there are other places that more explicitly discuss the use of a physiological salt concentration. There must be an explicit recommendation to only add enough ions to neutralize the system somewhere, because it's followed very widely.
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