Let me try to put my question in simpler words:
I use pbsa for calculating the electrostatic potential of proteins. How
can I enlarge the sampling volume (the absolute grid dimensions) for
this type of calculation? I tried `fillratio`, but failed.
Any suggestions would be helpful.
Thanks,
Jan-Philip
On 07/24/2012 07:13 PM, Jan-Philip Gehrcke wrote:
> Hello,
>
> I'd like to increase the grid dimensions in a PBSA run while keeping the
> spacing constant (just to see more of the distribution of the potential
> in space). I figured that this should be possible through the
> `fillratio` parameter. I did not find any other relevant parameter while
> browsing the documentation.
>
> Hence, I increased fillratio -- however, I did not observe a change in
> the grid dimensions in the DX output file. For my system, I get 55x69x63
> gridpoints in the DX file independent of the fillratio setting.
>
> So, my question is: how do I increase the grid dimensions in a way that
> a *larger* volume is sampled and that the data of the entire sampled
> volume is actually written to the volumetric data file?
>
> What follows now are some more details. I have played around a bit with
> the fillratio setting and used npbverb=1. What I've seen in the pbsa
> output file was the following:
>
> - "Grid dimension at level 2 55 69 63" did not change in
> dependence of fillratio. The data of this grid seems to end up in the DX
> file.
>
> - "Grid dimension at level 1 11 15 13" changes in dependence
> of fillratio (1.0 in this case).
>
> What are the two grid levels good for? Can you help me out here? The
> code in subroutine `pb_setgrd` is way too unstructured for me to follow
> its logic within a reasonable amount of time.
>
> Thanks,
>
> Jan-Philip
>
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Received on Mon Aug 20 2012 - 03:30:04 PDT
