I see, Thank you, professor!
A Merry Christmas and a wonderful New Year!
----- Original Message -----
From: <steinbrt.rci.rutgers.edu>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Thursday, December 22, 2011 4:11 PM
Subject: Re: [AMBER] Eptot is positive
> Hi,
>
>> 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,
>
> Thomas
>
> 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 - 23:30:03 PST
