AMBER Archive (2006)

Subject: Re: Re: AMBER: Pressure problem with restraint

From: Jianhui (
Date: Wed Oct 04 2006 - 14:24:35 CDT

Hello David,

>OK: this all sounds fine. I don't see any reason why the density should not
>equilibrate. You should look visually at the starting and ending structures
>(or at a movie of the trajectory) to see if something is funny. The initial
>isooctane geometry will probably be very bad, and it could be that it would
>take a very long time to equlibrate. If the geometries look very odd (with
>lots of holes or cavities), you might be better off to preprare a "Box" unit
>(from your simulation on pure isooctane) and then to solvate the micelle in
>that box (rather than in a single molecule). That would get you a much
By "solvate the micelle in that box" do you mean that I put the micelle into the equilibrated Isooctane box to solvate it?
Thank you.
>better starting structure.
>(I don't think the presence of absence of restraints on the micelle is
>relevant here.)
>...good luck...dac
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