[gmx-users] Conceptual question about the computational scaling of MD
mark.j.abraham at gmail.com
Sat May 11 20:53:55 CEST 2013
"for sure" is a bit of an overbid :) If the overall cost is dominated by
computation over the range of N of interest, then the scaling properties of
the computation will dominate the overall scaling.
On Sat, May 11, 2013 at 8:15 PM, francesco oteri
<francesco.oteri at gmail.com>wrote:
> Hi Andrew,
> maybe it is true on single processor simulations.
> It is false for sure when we talk about multicpu simulations because in
> this case each cpu has
> comunicate with each other and the implementations of this step makes a
> huge difference between
> the different codes.
> 2013/5/11 Andrew DeYoung <adeyoung at andrew.cmu.edu>
> > Hi,
> > Please forgive me for this slightly off-topic question. Suppose I use
> > particle mesh Ewald algorithm for the computation of electrostatic
> > interactions. It is often mentioned in the literature that the PME
> > algorithm scales as O(N logN), and that the electrostatic interactions
> > the most computationally expensive part of MD. Is it thus reasonable to
> > say
> > that MD overall scales as O(N logN)? Or does MD overall scale in some
> > other
> > way? I have been having difficulty finding a textbook or paper that
> > or estimates the scaling of MD.
> > Thank you so much for your time!
> > Andrew DeYoung
> > Carnegie Mellon University
> > --
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> Cordiali saluti, Dr.Oteri Francesco
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