There are a couple options. You can simply have a script that adds up all
of the other energy components (since each component goes up to 4 decimals,
you'll have a final energy that goes up to 4 decimals as well).
Alternatively, look at the "ntwe" variable and the "-e mden" output file
flags, which provides a detailed energy printout every "ntwe" steps, and
that should have much higher precision.
You should also note that I've only really seen this as a problem for
minimizations. In all dynamics simulations, you get printouts that contain
the total potential and kinetic energies (as well as their sum, if I'm not
mistaken). Therefore, only for minimizations will you be stuck in the
dilemma of having to choose between using "ntwe" to print out detailed
energy analysis or adding up every energy component to get 4 decimals of
precision in the total energy.
HTH,
Jason
On Mon, May 14, 2012 at 1:53 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Hi all,
>
> This may be a silly question, but in the manual or mailing list I couldn't
> find a simple way to print out the total energy of the system with sander
> with higher precision than given under "ENERGY" in the output (e.g. for
> minimization).
> The value under "ENERGY" is always in the scientific notification with 5
> significant numbers (e.g. -1.2345E+05).
> I would like to have the number with higher precision, e.g. -123456.7890.
> When nmropt is used, a value like this is printed under EAMBER, but only if
> you have non-zero values for your restraint force. So, a work-around would
> be to apply a very miniminal force to a distance of two ('uninmportant')
> atoms. But this is not ideal.
>
> Is there not an option or flag to simply print out the high precision total
> energy without such a work-around?
>
> Thanks and apologies if I've overlooked something...
> Marc
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 14 2012 - 06:00:07 PDT
