Hi,
There is likely a bug in the code used to integrate the RDF. I will
look into it. Thanks.
-Dan
On Tue, Jun 18, 2013 at 10:42 AM, Domenico Marson
<domenico.marson.phd.units.it> wrote:
> Dear Amber Users,
>
> I'm using "radial" function with both ptraj and cpptraj (AT-13 with
> all latest bugfixes to date) to estimate the number of water molecules
> (:WAT) around a residue of my protein (:92).
> After loading 10 frames from my simulation I used the following commands:
>
> with PTRAJ
>> image
>> radial pt_2 0.2 15.0 :WAT :92 noimage
>> radial pt_1 0.1 15.0 :WAT :92 noimage
>
> with CPPTRAJ
>> radial cppt_02.out 0.2 15.0 :WAT :92 intrdf cppt_02.out
>> radial cppt_01.out 0.1 15.0 :WAT :92 intrdf cppt_01.out
>
> >From the mailing list I understood that the last column in ptraj
> output represents the integral (or effectively the occupancy as a
> function of distance or loosely how many waters in a shell of a given
> radius), and also with the "intrdf" option I expect cpptraj to print
> the same information in the output file.
>
> Comparing the outputs from ptraj (standard normalization) and cpptraj
> I saw that the RDF values are in agreement with each other, as
> expected, but that the integral values are very different.
> Also, doubling the bin spacing leads to a doubling of the integral
> values in cpptraj output, while integral values from ptraj are almost
> unchanged.
>
> I also approximated by hand the integral with the trapezoid rule (from
> the RDF values), and I obtained a reasonable result with both 0.1 and
> 0.2 bin spacing.
>
> So, in conclusion, I'm asking if someone in the list can clarify to me
> why the integral values are so different from ptraj and cpptraj, and
> on which value I have to rely to have an approximation of the number
> of water molecules around my residue.
>
> Thank you in advance for any help,
>
> Domenico
>
> --
>
> Domenico Marson
> Ph.D. student
> Molecular Simulation Engineering (MOSE) Laboratory
> Department of Engineering and Architecture - DEA
> University of Trieste
> Via Valerio, 10
> 34127 - Trieste (Italy)
> Phone: +39 040 5583757
> Skype: domenicomars
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Jun 18 2013 - 11:00:02 PDT
