Jan-Philip,
Do you mean to use a different fillratio? I suppose you can use any
reasonable number, i.e. larger than 1.0.
All the best,
Ray
On Wed, Sep 12, 2012 at 9:41 AM, Jan-Philip Gehrcke
<jgehrcke.googlemail.com> wrote:
> 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 - 10:30:03 PDT
