Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)?

From: Jan-Philip Gehrcke <>
Date: Mon, 20 Aug 2012 12:24:49 +0200

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.



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
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