VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Apr 28 2012 - 12:33:09 CDT

On Sat, Apr 28, 2012 at 12:17 PM, Emiliano Ippoliti
<e.ippoliti_at_grs-sim.de> wrote:
> Hi Axel,
>

> 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.

no. it is not doing the *exact* same thing as in VMD 1.9.1,
since there were bugs in the normalization as well. i don't
recall the exact sequence of events and how we eliminated
all the bugs, but according to the cvs log it was in several
iterations. between 2006 and 2008, so quite a while back
and before and after the release of VMD 1.8.6 (which was
in 2007).

>>
>>> 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?

yes.

>>> 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... :-)

yes, there is no way to make this kind of code work efficiently in Tcl.

ciao,
    axel.

>> axel.
>>
>
> Best,
> Emiliano
> 

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