normal charged small molecule parameterization

  • Junb
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8 months 1 week ago #9401 by Junb
Dear Martini developer,

I was thinking to model a charged small molecule (such as +3 charges), using Martini 3 parametrizing approach mentioned in the tutorial. I wonder if I need to add ions (such as only 3 chloride atomistic ions?) to neutralize the system when I run the atomistic simulation as the reference for CG parametrization.

Then when I run and finalize the CG model, and optimize the CG parameters, do I need to also include the equal number of ions (such as only 3 chloride CG ions)? Thanks in advance.

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8 months 1 week ago #9402 by riccardo
Replied by riccardo on topic charged small molecule parameterization
Yes, I would do that - add 3 ions both in the AA and CG systems, so that your system is neutral.

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8 months 1 week ago #9404 by Junb
Replied by Junb on topic charged small molecule parameterization
Thanks so much! I appreciate your help.

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