AMBER Archive (2006)

Subject: AMBER: potential energy

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Sep 17 2006 - 19:38:44 CDT

Dear All,

For the results of MD,there are kinetic energy,
potential energy and relative energy. I think all
these should be relative quantity. Will you please
tell me in which state the protein has absolute 0
energy?

After energy minimization, we get a protein
conformation with the lowest energy and this number is
usually negative. Can we difine the energy in this
conformation as 0 energy? For the kinetics energy, it
should has some relation with the velocity, however
the initial velocity is produced randomly. Does this
means that the initial kinetic energy will be a random
value?

I am looking somebody to clarify these.

Best regards.

Fenghui Fan

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