VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Apr 28 2012 - 10:11:58 CDT

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.

> 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.

> 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"?

axel.

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