Ray,
Actually I missed your answer below. Excuse me. I will look into how
nfocus changes the behavior I observed. Do you expect fillratio to have
no effect with nfocus=2?
Thank you!
Jan-Philip
On 08/22/2012 04:25 PM, Ray Luo wrote:
> I think fill ratio is the only thing you need to worry about. Of course you don't want to turn on electrostatic focusing, ie nfocus should be set to 1.
>
> Ray Luo, Ph.D.
>
> On Aug 20, 2012, at 6:24 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com> 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 - 11:00:04 PDT
