Re: [AMBER] Eptot is positive

From: <>
Date: Thu, 22 Dec 2011 03:11:51 -0500 (EST)


> Although the Eptot is positive, the run keep steady up to this point. is
> this normal? and why?

The potential energy of a force field is given with respect to an
arbitrary zero, so the absolute value will not tell you anything. Bond
parameters are e.g. all set so that their minima correspond to zero, not
the true bonding energy.

As always in physical chemistry, a total energy is not useful unless you
have some other energy to compare to (and a process connecting both).

Therefore, I would assume that all is well with your simulation :-)

Happy holidays,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Dec 22 2011 - 00:30:03 PST
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