[gmx-users] Conceptual question about the computational scaling of MD

francesco oteri francesco.oteri at gmail.com
Sat May 11 20:15:15 CEST 2013

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 the
> 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 are
> 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 states
> 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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