Thanks!!!
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Saturday, June 27, 2020 6:53:01 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] restraining surfactant tails in micelles intact
On Fri, Jun 26, 2020, Billiot, Eugene wrote:
>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.
I think you'll have to examine a snapshot of the structure, and choose
which tails you want to "connect" (i.e. to model as polymerized). How
many such bonds do you think are formed, and which ones are they?
Once you have decided that, just use an "NMR" distance restraint to keep
the atom pairs you have chosen to stay fairly close together. You
probably don't need to model the chemistry: just keep the relevant atom
pairs at about the sum of their van der Waals radii apart. I don't
immediately see how any COM-type restraint would be of much help here,
but maybe others on the list have some relevant experience or ideas.
....dac
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Received on Sat Jun 27 2020 - 08:30:03 PDT
