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

From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Tue, 24 Jul 2012 19:13:00 +0200

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 Tue Jul 24 2012 - 10:30:03 PDT
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