Re: [Apbs-users] about glen parameters.

[Todd D. <to...@cc...>]

Hi Changhui -

The glen parameter sets the grid length, which effectively sets the grid
spacing for a particular mg-manual run of APBS.  Thus when you vary the
glen, you're varying the grid spacing and accuracy of the run.  The
Python script psize.py (apbs/tools/manip/psize.py) can help you pick an
appropriate glen.  Following through using the ion-protein/small491.pqr
example, running psize on that file yields a recommended

Coarse grid dims = 66.142 x 67.701 x 74.474 A
Fine grid dims = 58.907 x 59.824 x 63.808 A

or a glen of roughly 67 67 75, which is what is found in the ion-protein
example's input file.

You can also use apbs/tools/manip/inputgen.py, which uses the
information obtained from psize to create an initial recommended input
file.

Hope this helps -

Todd

On Thu, 2004-07-08 at 13:56, changhui yan wrote:
> I used following input file to calculate the electrostatic potential for the 
> protein (apbs-0.3.1/examples/ion-protein/small491.pqr) that come with  the 
> document examples.  I tried three different sets of glen:
> 
> glen 50 50 50
> glen 70 70 70
> gen 90 90 90
> 
> I found that there are big difference in the results when I use different 
> glen parameters.   Why is that? How should I set the glen parameter for a 
> new protein?
> 
> Thank you very much!
> 
> --changhui
> 
> P.S.  (apbs.in )
> 
> read
>     mol pqr small491.pqr
> end
> 
> # ENERGY OF PROTEIN CHUNK
> elec name protein
>     mg-manual
>     dime  129 129 129
>     glen  90  90  90
>     gcent mol 1
>     mol 1
>     npbe
>     bcfl sdh
>     ion 1 0.050 2.0
>     ion -1 0.050 2.0
>     pdie 2.0
>     sdie 78.4
>     chgm spl0
>     srfm smol
>     srad 1.4
>     swin 0.3
>     temp 298.15
>     gamma 0.105
>     calcenergy comps
>     calcforce no
> end
> #
> print energy protein end
> 
> quit
> 
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