Re: NAMD FFTW question?

From: Gianluca Interlandi (
Date: Fri Aug 07 2009 - 12:54:26 CDT

FFTW stands for "Fastest Fourier Transform in the West". It can be done
only in a system with periodic boundary conditions which you have only
with a water box. It's a method to efficiently calculate Particle Mesh
Ewald which is used to evaluate long range electrostatics. I recommend you
borrow the book "Understanding molecular simulation" by Frenkel & Smit, AP
Press. Everything is explained in there with all the details.

Have fun,


On Fri, 7 Aug 2009, snoze pa wrote:

> Dear NAMD users,
> Just a quick question about the NAMD FFTW calculation. Why NAMD is
> not creating FFTW_NAMD*.txt file when we use water in sphere while it
> creates a FFTW_NAMD file when we use water in box. Any comments?
> Thank you
> s

Gianluca Interlandi, PhD
                     +1 (206) 685 4435
                     +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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