[gmx-users] rdf doesn't tend to unity
ester.chiessi at uniroma2.it
Tue Sep 13 18:13:58 CEST 2005
----- Original Message -----
From: "David" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Tuesday, September 13, 2005 4:36 PM
Subject: Re: [gmx-users] rdf doesn't tend to unity
>> >> >> I calculated the MD of a polymeric network in SPC water. I was very
>> >> >> surprised when I found that the rdf between the oxygen atoms of the
>> >> >> polymer
>> >> >> and the water oxygen atoms doesn't reach the value of 1 at high r
>> >> >> values.
>> >> >> The g(r) remains lower than unity and tends to 0.87.
>> >> >> I could expect a value higher than 1, eventually for inhomogeneity,
>> >> >> but
>> >> >> not
>> >> >> lower.
>> >> > Test whether the integral (4 pi r^2 g(r)) goes to #Ow
>> >> The number of polymer oxygens is 611.
>> >> OW number is 8773.
>> >> The box is cubic with size of 6.707 nm.
>> >> The integral in the 0-3.3535 nm distance interval results 136.16 nm^3.
>> > It should go to 8773, did you include the terms above in the integral?
>> I calculated the integral of (4 pi r^2 g(r)) with r from 0 to 3.3535
>> and the result was 136.16 nm^3.
>> If you multiply this value for #OW and divide for the box volume, you
>> a number of oxygens (3959) lower than that you can estimate (4593) by
>> considering a sphere of water with radius 3.3535 and density equal to the
>> water average density in the box.
>> The ratio 3959/4593 is 0.86, the limiting value of g(r). If it is not a
>> chance, what could it mean?
> It's correct. Do you have a cluster of polymer surrounded by water?
Thanks for your interest.
Some polymer regions are aggregated, some others more extended.
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> No virus found in this incoming message.
> Checked by AVG Anti-Virus.
> Version: 7.0.344 / Virus Database: 267.10.21/96 - Release Date: 10/09/2005
More information about the gromacs.org_gmx-users