perhaps you want relative free energies of families of conformations,
in which case you might be able to use their relative populations
to calculate free energies. As Dave says, it might help if you can
be much more specific about what data you have and what you want
to calculate, and for what purpose.
carlos
On Nov 21, 2007 2:42 PM, David A. Case <case.scripps.edu> wrote:
> On Tue, Nov 20, 2007, huzehan19870731.126.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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Received on Sun Nov 25 2007 - 06:07:12 PST
