Hi Dr. Steinbrecher,
thanks so much for answering!
-Dave
On Fri, Sep 16, 2011 at 7:16 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > Just as a rough estimate, how much time of a computation does each of
> > these
> > terms take? Which is the most costly/cheap?
>
> To give a one sentence answer, the non-bonded terms (Coulomb&LJ) take up
> by far (>90%) the largest part of a (non-polarizable, non QM/MM)
> calculation. These further split into direct sum (LJ and Coulomb up to
> cutoff) and reciprocal (the Fourier space part of PME), of which direct
> sum takes very roughly about 60%. In extreme cases, depending on the write
> frequency and number of MPI threads, your job speed may depend more on
> interconnect and disk speed than on actually doing the claculations.
>
> But note that any amber calculation will contain precisely this
> information at the end of mdout, so you can check for you own system and
> parameter settings...
>
> Kind Regards,
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Fri Sep 16 2011 - 17:30:02 PDT
