VMD-L Mailing List

From: Emiliano Ippoliti (e.ippoliti_at_grs-sim.de)
Date: Sat Apr 28 2012 - 11:17:00 CDT

Hi Axel,

On Apr 28, 2012, at 5:11 PM, Axel Kohlmeyer wrote:

> On Sat, Apr 28, 2012 at 9:51 AM, Emiliano Ippoliti
> <e.ippoliti_at_grs-sim.de> wrote:
>> Hi Everyone,
>>
>> I noticed that starting from VMD 1.8.7 the behavior of the "measure gofr" command in the TkConsole is slightly changed.
>> In particular, if I calculate a radial distribution function by VMD 1.8.6 and I impose STEP 0.03, I get a function described by the values at the points on the x-axis:
>>
>> 0.03 0.06 0.09 ...
>>
>> If I use VMD 1.8.7 or later versions I get a function described by the values at the points on the x-axis:
>>
>> 0.015 0.045 0.075 ...
>>
>> (in general the points on the x-axis are STEP/2 STEP/2+STEP STEP/2+2*STEP ...)
>>
>> Is this weird (for me) behavior coded on purpose?
>
> yes. it was done on purpose and not weird at all.
> the g(r) is based on histogramming and the center
> of a histogram bin is a much better representation
> of it than its left (or right) boundary.

I see, and this is logic.
But so now I am wondering what is VMD1.8.6 calculating? If it is doing the same thing as the later version (i.e. binning in [0, 0.03] [0.03, 0.06] ...) and simply reporting the right boundary of the bin in place of its center, I would expect to have the same values for the gofr but this is not true. I noticed slightly different values for the corresponding bins by analyzing the same trajectory with VMD1.8.6 and VMD1.9b3.

>
>> Is there a simple way to restore the previous "plain" behavior apart from using VMD 1.8.6?
>> (In practice I need to translate each point of the fixed amount STEP/2)
>
> it is a constant offset.
>

Yes, exactly. Or in other words I need that the recent VMD version starts creating histogram bins from the offset and not from the origin, so that the centers of the histogram bins are in the positions I need.
I guess that an "rmin" option is not implemented and I have to code, isn't it?

>> I am not familiar with the VMD code but in case, where can I found the part of the code where is implemented the gofr calculation?
>
> TclMeasure.C, Measure.[Ch] and MeasureRDF.C plus CUDAMeasureRDF.cu
> for the GPU version.
>
> ever heard of the tool "grep"?
>

So, it is coded in C... now I understand why I had no results by grepping on the tcl files... :-)

> axel.
>

Best,
Emiliano

>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

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Dr. Emiliano Ippoliti
Research Associate

German Research School for
Simulation Sciences GmbH
52425 Jülich | Germany

Members: Forschungszentrum Jülich GmbH | RWTH Aachen University
Tel: +49 2461 61 8920
Email: e.ippoliti_at_grs-sim.de
Web: www.grs-sim.de

Members: Forschungszentrum Jülich GmbH | RWTH Aachen University
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Düren (Amtsgericht Düren) under registration number HRB 5268
Registered office: Jülich
Executive board: Prof. Marek Behr Ph.D. | Dr. Norbert Drewes

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