On Fri, Jul 29, 2016 at 7:56 AM, Markus Schneider
<markus.schneider2.mytum.de> wrote:
> The results I generated with your new cpptraj version are now in
> agreement with my own numbers. On a related note, I noticed that those
> lines directly before the changed code:
>
> if (firstvalue < 0) firstvalue += 360;
> prevbin = (int) (firstvalue - 30.0) / 60;I would guess the if clause
> should be changed to (firstvalue < 30) as well?
Yes, good catch. This would affect the first transition only, but
better to be 100% correct. Thanks again!
-Dan
>
>
> Glad to be of help!
>
> Markus
>
> Am 07/29/2016 um 01:00 AM schrieb Daniel Roe:
>> 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)
>>
>>
>
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--
-------------------------
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 Fri Jul 29 2016 - 07:30:02 PDT
