Re: Setting PME Grid

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 30 2009 - 12:52:09 CDT

According to the documentation:

     If any of the grid sizes below are not set, then PMEGridSpacing must
     be set (recommended value is 1.0 ) and will be used to calculate
     them.

So, by using PMEGridSpacing NAMD will probably try to calculate optimal
PMEGridSizeX,Y,Z, probably also taking into account the fact that they
should have only small integer factors (2, 3 and 5), I imagine. One should
look at the code to be sure, though. On the other hand, by specifying
PMEGridSizeX,Y,Z the user will have more control.

Have you tried specifying PMEGridSpacing and looking at the NAMD log to
see what PMEGridSizeX,Y,Z were calculated?

Hope this helped.

Gianluca

On Thu, 30 Apr 2009, DimitryASuplatov wrote:

> Hello,
>
> is there any significant difference between using
>
> PMEGridSpacing 1.0
>
> and
>
> PMEGridSizeX X
> PMEGridSizeY Y
> PMEGridSizeZ Z
>
> The first looks more appropriate for writing automation though in
> absolute majority of NAMD config files on the internet the second is
> used. Why?
>
> Thanks,
> SDA
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     +1 (206) 714 4303
                     http://artemide.bioeng.washington.edu/

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