Dear PBSA developers,
this will be the last time I ask, promised. Can you think of a way to
modify the size of the sampling space (the grid dimensions) in PBSA
calculations?
If you don't know or think there is no way or if my question is still
unclear please drop me a line. Any answer is helpful.
Thanks!
Jan-Philip
On 08/20/2012 12:24 PM, Jan-Philip Gehrcke wrote:
> 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 Wed Sep 12 2012 - 10:00:02 PDT
