Re: [AMBER] binding free energy and pose analysis

From: case <>
Date: Sat, 28 Dec 2013 08:38:04 -0500

On Sat, Dec 28, 2013, Nitin Sharma wrote:
> Can you tell me if it will correct approach to combine MD and simulated
> annealing trajectories?

For most purposes, "no". Simulated annealing trajectories explore a variety
of temperatures, in an effort to find an optimal structure. They are not
appropriate for use in (say) binding free energy calculations, which are based
on an approach that makes use of Boltzmann sampling at a *single* temperature.


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Received on Sat Dec 28 2013 - 06:00:03 PST
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