[AMBER] restraining surfactant tails in micelles intact

From: Billiot, Eugene <Eugene.Billiot.tamucc.edu>
Date: Fri, 26 Jun 2020 19:55:41 +0000

Hello Folks,
I am trying to mimic "molecular micelle" systems where experimentally we have a double bond at the end of the hydrophobic tail "in the center of the micelle" and we then subject the solution which as significantly higher than the critical micelle concentration to radiation which causes free radical polymerization. This process keeps the surfactant micelles within the micelle from dissociating. They are essentially "locked into the micellar form." My question to this group is once I form the micelles (in my case I use the online tool Micelle-Maker to form the micelles) how do I keep the surfactant tails from migrating away from one another to mimic a polymerized/molecular micelle during simulation. What command do I use. I know Amber has restraint or constraint options and I assume I would restrain the atoms at the end of the tails, but I do not if it is best to use center of mass or center of geometry or some other option to try to do this. I have read through the Amber manual (section 25.1. Distance,
 angle and torsional restraints) about how to use restraints/constraints but I cannot figure out how to apply that to the system I am trying to study. Any help would be greatly appreciated.

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Received on Fri Jun 26 2020 - 13:00:02 PDT
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