normal MARTINI3 CG model for perfluorooctane (C8F18)

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1 year 7 months ago #9539 by hsk81123
I have two questions regarding the MARTINI 3 CG model for perfluorooctane (C8F18 or CF3-(CF2)6-CF3)

1. For CF3 atoms, can I use the SX4e bead to represent the CF3 of perfluorooctane, as suggested in the following paper about the MARTINI 3 small molecules? (page 7 of Adv. Theory Simul. 2022, 5, 2100391)

2. For CF2 atoms, does it make sense to represent each CF2 as one bead, or several CF2 atoms (such as (CF2)3) as one bead?

Thank you!

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1 year 6 months ago #9541 by vainikka
Replied by vainikka on topic MARTINI3 CG model for perfluorooctane (C8F18)
Hi,

1. Yes, CF3 is typically represented as SX4e, although the 'e'-label might not be applicable in your particular system.

2. I would start mapping with each CF2 as a small bead. Grouping multiple CF2 units to a single bead wouldn't make much sense to me.

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1 year 6 months ago #9542 by hsk81123
Replied by hsk81123 on topic MARTINI3 CG model for perfluorooctane (C8F18)
I see. Thank you so much for your reply!

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9 months 19 hours ago #9675 by Imamul
2. For CF2 atoms, does it make sense to represent each CF2 as one bead, or several CF2 atoms (such as (CF2)3) as one bead?

Have you got any other suggestions except from vainikka?
I am also looking for CF2 bead-type of octafluoropropane molecule.

regards
Imamul

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