AMBER Archive (2007)

Subject: Re: AMBER: equilibration in explicit solvent

From: David A. Case (case_at_scripps.edu)
Date: Sun Feb 04 2007 - 23:27:44 CST

On Sun, Feb 04, 2007, Amarda Shehu wrote:
>
> These two conformations have been obtained with a newly developed method
> in implicit solvent (using ff03 and GB). I am preparing a manuscript for
> publication, but my advisor has asked me to make sure that in explicit
> solvent, these conformations retain both their structural integrity and
> their energetic difference.

Even if you did everything you originally suggested, you would only get the
*potential* energy difference between the two solvated systems. But the
implicit solvent calculation estimates the *free* energy of the solvent.
The difference is the entropy effect, mentioned by Prof. Duan.

Testing the structural integrity is straightforward, and it sounds like you
have already done that. Getting a comparable energetic number is more
involved. It sounds like you probably want to think about a thermodynamic
integration calculation to compute the free energy difference between the two
solutes.

....good luck...dac

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