AMBER Archive (2004)

Subject: Re: AMBER: Using gibbs to calculate free energy

From: David A. Case (
Date: Fri Jun 18 2004 - 10:14:55 CDT

On Fri, Jun 18, 2004, Xioling Chuang wrote:
> However, I would like to
> calculate the free energy of dimer with 2 conformations in explicit solvent;
> (I). state 0 := monomer1 is on top of monomer2 as parallel conformation
> (II). state 1 := monomer1 is on top of monomer2, but twist angle between 2
> monomers is 180 degree (antiparallel conformation)

This is a problem that would usually be tackled by umbrella sampling (or
perhaps by MM-PBSA). Changing from one conformation to another is not
something you would want to use the perturabtion facilities in gibbs for.

...good luck...dac

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