## VMD-L Mailing List

**From:** Ivan Vyalov (*vyalov_at_mis.mpg.de*)

**Date:** Fri Apr 20 2012 - 14:49:21 CDT

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

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):
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*>> img812.imageshack.us/img812/2722/handintegral.png
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*>>
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*>> 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
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*>> If I average more taking wider bins I get the following picture:
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*>> img252.imageshack.us/img252/8083/htailbroadbin.png
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*>>
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*>>
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*>> This looks quite strange even though I know about difficulties with such calculations.
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*>> The question is obvious, is everything alright with the normalization of g(r) in VMD?
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*>>
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*>> However, it can be something else rather than normalization because functions of different pairs behave differently:
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*>> img191.imageshack.us/img191/8205/handintegralall.png
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*>> This means that OO and HH have positive component in h(r) and OH -- negative.
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*>>
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*>> Any help and ideas are much appreciated!
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*>>
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*>> 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

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