VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Apr 20 2012 - 14:11:28 CDT

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