Re: PME questions

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Aug 28 2008 - 12:39:31 CDT

You want to make sure that the prime factor decomposition of your PME grid
dimensions contains only powers of 2, 3 and 5. You also want to make sure
that the ratio between the basic vector length and the PME grid dimension
is 1 or less. For example, if your basic vector length is 78.5 you want to
choose 80 as your PME grid dimension.

Gianluca

On Thu, 28 Aug 2008, Lam T Nguyen wrote:

> Hello,
>
> The NAMD tutorial says that "PME grid dimensions should have small integer
> factors only and be greater than or equal to length of the basis vector"
>
> I wonder, why we compare the grid dimensions, which are integers, to the
> basic vector length? Can you explain more about choosing the PME grid size?
>
> PME is a fast method. But when I tested it, it turned out very slow. I tried
> changing fullElectFrequency, cutoff, gridspacing but it did not help much.
>
> Thanks,
>
> Lam
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     +1 (206) 714 4303
                     http://biocroma.unizh.ch/gianluca/

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