## VMD-L Mailing List

**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Fri Apr 20 2012 - 17:50:26 CDT

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On Fri, Apr 20, 2012 at 3:49 PM, Ivan Vyalov <vyalov_at_mis.mpg.de> wrote:

*> On 04/20/2012 09:11 PM, Axel Kohlmeyer wrote:
*

*>>
*

*>>
*

*>> On Apr 20, 2012, at 6:43 AM, Ivan Vyalov<vyalov_at_mis.mpg.de> wrote:
*

*>>
*

*>>> Hi all!
*

*>>>
*

*>>>
*

*>>> I have a question related to the normalization of rdf in VMD. I've seen
*

*>>> the previous thread about it
*

*>>> www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/18223.html
*

*>>> but it seems that problem of opener has disappeared but mine is still
*

*>>> here. I get the same problem with limiting behaviour of g(r).
*

*>>
*

*>> Which version of VMD are you using?
*

*>>
*

*>> How do you compute the integral?
*

*>> The value of g(r) is binned and the r is taken as the center of the bin.
*

*>>
*

*>> Axel
*

*>>
*

*>>> The system is 4169 SPC/E water molecules at 306 K in the box with cell
*

*>>> length 50 \AA{}.
*

*>>> What I need is to calculate Kirkwood-Buff integral. h(r) looks well in
*

*>>> general:
*

*>>> img846.imageshack.us/img846/6460/56853809.png
*

*>>> but its integral multiplied by r^2 diverges(here it's just a sum h(r)r^2
*

*>>> not multiplied by dr and is a little bigger than the proper integral, but it
*

*>>> doesn't change the problem):
*

*>>> img812.imageshack.us/img812/2722/handintegral.png
*

*>>>
*

*>>> At first, I equilibrated system for 1ns, but when I've obtained this
*

*>>> behaviour I continued to equilibrate for 2 ns more with the same result.
*

*>>> Here is the tail of h(r) which is noisy but definitely lies above zero in
*

*>>> average.
*

*>>> img210.imageshack.us/img210/9803/htail.png
*

*>>> If I average more taking wider bins I get the following picture:
*

*>>> img252.imageshack.us/img252/8083/htailbroadbin.png
*

*>>>
*

*>>>
*

*>>> This looks quite strange even though I know about difficulties with such
*

*>>> calculations.
*

*>>> The question is obvious, is everything alright with the normalization of
*

*>>> g(r) in VMD?
*

*>>>
*

*>>> However, it can be something else rather than normalization because
*

*>>> functions of different pairs behave differently:
*

*>>> img191.imageshack.us/img191/8205/handintegralall.png
*

*>>> This means that OO and HH have positive component in h(r) and OH --
*

*>>> negative.
*

*>>>
*

*>>> Any help and ideas are much appreciated!
*

*>>>
*

*>>> thanks in advance,
*

*>>> Ivan
*

*>
*

*>
*

*> Hello Axel,
*

*>
*

*> I used VMD 1.9 and 1.9.1 and they both give the same result.
*

*>
*

*> Here's the better plot of integral calculated as (scipy)
*

*> cumsum(h*r**2*(r[1]-r[0]))
*

*> http://img62.imageshack.us/img62/9466/handrightintegral.png
*

*>
*

*> The problem comes from positive tail in h, can it be from PME(I took grid
*

*> spacing equal to 1\AA{})? From the other hand if I take the average of h(r)
*

*> from 15 to 25 \AA{} and subtract it from h(r), integral converges and it
*

*> seems to me that the error is constant.
*

*> http://img401.imageshack.us/img401/871/hshiftedandrightintegra.png
*

can you please try running your g(r) calculation with a smaller

bin size, say 0.01 instead of the default of 0.1?

and let us know if that makes matters better or

worse or has no impact at all.

thanks,

axel.

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

**Next message:**Axel Kohlmeyer: "Re: HOOMD problems"**Previous message:**John Stone: "Re: Anaglyph stereo with other colors"**In reply to:**Ivan Vyalov: "Re: gofr limit, Kirkwood-Buff integrals"**Next in thread:**Ivan Vyalov: "Re: gofr limit, Kirkwood-Buff integrals"**Reply:**Ivan Vyalov: "Re: gofr limit, Kirkwood-Buff integrals"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]