unanswered Hybrid model with cholesterol separated by user defined bonds

  • nambinik
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2 years 2 months ago #9341 by nambinik
Hi, I have created a model with 2 cholesterol molecules connected via a user defined bond between ROH atoms to mimic cholesterol on a scaffold.

I've added a PO4 molecule in between the ROH molecules. Ie the ROH-PO4-ROH bond. I've played around with the bond length and bond angle forces to mimic the system I want.

Is there something I should keep in mind about this system, especially when calculating free energy interactions?

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