AMBER Archive (2006)

Subject: Re: AMBER: Pressure problem with restraint

From: David A. Case (
Date: Wed Oct 04 2006 - 10:06:38 CDT

On Tue, Oct 03, 2006, Jianhui wrote:
> I solvated a reverse micelle (RM) with apolar solvent. What I do is first
> to constrain the reverse micelle part and run MD under 300k and 1 atm to
> equilibrate the solvent to the equilibrium density. The problem is that
> with RM constraint here the apolar solvent didn't come down to the expected
> density. So I wonder how the constraint actually affacted the pressure and
> density? Is there another way that I can accomplish what I want to do?

It's hard to say much without more information: how much solvent was there,
relative to micelle? what is the solvent? do you know that you get a
correct density in a pure solvent simulation? What kind of constraints
(restraints?) did you use? How far off was the density? How do you know
what the "correct" value is (i.e. with the micelle present)? And so on.


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