AMBER Archive (2007)

Subject: Re: AMBER:How to calculate the free energy of a series of conformations

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 21 2007 - 13:42:09 CST

On Tue, Nov 20, 2007, huzehan19870731_at_126.com wrote:
>
> I'm a new AMBER user, and I am trying to calculating the free energy of
> each conformation in a trajactory simulated by conventional MD.

This is not a correctly-formulated problem: individual conformations do not
have free energies. Free energy is a property of some ensemble of structures.

Can you state more precisely what you are looking for? What do you plan to do
with the values you would get?

...dac

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