AMBER Archive (2006)

Subject: Re: AMBER: Pressure problem with restraint

From: David A. Case (
Date: Wed Oct 04 2006 - 13:03:45 CDT

On Wed, Oct 04, 2006, Jianhui wrote:
> The solvent I used is Isooctane, in pure solvent simulation the density
> comes to 0.7100 g/cm3 consistant with the experiment data. I used xleap
> command: "Solventbox RM Isooctane 20" to solvate the RM with Isooctane. In
> the command, "Isooctane" is just one molecule of Isooctane. Then I minimize
> the system and do MD with "ntr=1, restraint_wt=10.0,
> restraintmask=':1-448'" to restraint the RM and let the solvent equilibrate
> first under 300K and 1atm. The starting density of the system will be
> 0.4899 and the density will increase slightly and then come down to 0.4900.
> The density of RM and isooctane is expected to be about 0.7520. The molar
> ratio of solvent to RM surfactant is about 25:1. I hope these information
> can help to clarify my question.

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
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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