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?
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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Received on Fri Jul 29 2016 - 07:30:02 PDT
