Hi,
I think I've got this fixed in the GitHub version of cpptraj. If you
get a chance, would you mind trying the calculation again with this
code?
https://github.com/Amber-MD/cpptraj
Thanks again for the report,
-Dan
On Thu, Jul 28, 2016 at 4:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> This bug is confirmed. The issue is that this line:
>
> if (dval < 0) dval += 360;
>
> should actually be:
>
> if (dval < 30) dval += 360;
>
> in order to ensure that values below 30 end up in bin 5 (c) instead of
> bin 0 (g+). This bug appears to have been present since ptraj. I'll
> start working on a fix. Thanks for the report!
>
> -Dan
>
>
> On Thu, Jul 28, 2016 at 3:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> There does seem to be a problem. I'll look into it further and get
>> back to you. Thanks for the report.
>>
>> -Dan
>>
>> On Fri, Jul 22, 2016 at 6:22 AM, Markus Schneider
>> <markus.schneider2.mytum.de> wrote:
>>> Hi,
>>>
>>> during analysis of "multidihedral" generated torsion datasets with the
>>> "stat" command, I encountered an unexpected result. Compared to my own
>>> calculations, the "c" and "g+" bin occupancies are different. I expected
>>> that the "c" bin would contain angles from -30 to +30 deg and "g+" would
>>> contain the range from +30 to +90 deg.
>>>
>>> The raw multidihedral output data is in the range [-180,+180]. When I
>>> bin the raw data myself, I can reproduce the result of cpptraj's stat
>>> analysis exactly if I set the c bin to [-30,0] and the g+ bin to [0,90].
>>> When I set the bins to the expected values above, I get more data points
>>> in the c bin, while fewer are placed in the g+ bin. I would like to ask
>>> whether there might be an error with how the stat command bins the data.
>>>
>>> The relevant code piece in Analysis_Statistics.cpp seems to be:
>>>
>>> double value = ds.Dval( i );
>>> double dval = value;
>>> if (dval < 0) dval += 360;
>>> *curbin = (int) (dval - 30.0) / 60;*
>>>
>>> I suspect that the last line might be responsible for the observation.
>>> The first three lines, as I infer, provide that dval is transformed to
>>> the range [0,360]. I created a test in C for the last line:
>>>
>>> --------------
>>>
>>> int bin(double angle)
>>> {
>>> return (int) (angle - 30.0) / 60;
>>> }
>>>
>>> int main()
>>> {
>>> double angles[] = {0.0,29.0,30.0,89.0,90.0,149.0,
>>> 150.0,209.0,210.0,269.0,270.0,329.0,330.0,359.0};
>>> for(int i=0;i<14;i++){
>>> printf("angle: %.1f bin: %d\n",angles[i],bin(angles[i]));
>>> }
>>>
>>> return 0;
>>> }
>>>
>>> --------------
>>>
>>> which creates the following output:
>>>
>>> angle: 0.0 bin: 0
>>> angle: 29.0 bin: 0
>>> angle: 30.0 bin: 0
>>> angle: 89.0 bin: 0
>>> angle: 90.0 bin: 1
>>> angle: 149.0 bin: 1
>>> angle: 150.0 bin: 2
>>> angle: 209.0 bin: 2
>>> angle: 210.0 bin: 3
>>> angle: 269.0 bin: 3
>>> angle: 270.0 bin: 4
>>> angle: 329.0 bin: 4
>>> angle: 330.0 bin: 5
>>> angle: 359.0 bin: 5
>>>
>>> According to bin definitions above, I expect that the angles 0 and 29
>>> deg should be part of bin 5. Instead, it seems that stat's g+ bin (0)
>>> ranges from 0 to 90, while the c bin (5) ranges from 330 to 0. This is
>>> consistent with my manual calculations. What do you think about this?
>>>
>>> This was tested with a fresh build of AmberTools 16.
>>>
>>> Best,
>>>
>>> Markus
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jul 28 2016 - 16:30:02 PDT
