Ray,
thanks for your response. I already tried to achieve what I want using
`fillratio` -- but failed. I described what I did in my initial mail
from 07/24/2012 (see below).
Thanks for your help!
Jan-Philip
On 09/12/2012 07:10 PM, Ray Luo, Ph.D. wrote:
> 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 - 10:30:05 PDT
