AMBER Archive (2006)

Subject: Re: AMBER: AMBER 8.0 : Octane Implicit Solvent?

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 24 2006 - 13:09:32 CST

On Tue, Jan 24, 2006, Guillaume Bollot wrote:

> I would like to perform simulations of a protein in implicit solvent to see
> the effects between water and octane. I used IGB=1 and I changed
> EXTDIEL=2.0 for the octane but I didn't find the EXTDIEL in the mdout file.
> This is the same case for water where EXTDIEL=78.5 (default). How to know
> if my simulation is carried out in octane?

The extdiel value is indeed used, although it is not printed; (this will be
fixed in the next release). You can check this by examining the code, or
just by running a short simulation (or a single point) with various values of
extdiel to see what happens.

However, it is by no means sure that just setting an appropriate value of
extdiel will give you results characteristic of octane; I don't think this has
ever been tested. So, please proceed with caution.

...regards...dac

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