VMD-L Mailing List

From: Ivan Vyalov (vyalov_at_mis.mpg.de)
Date: Fri Apr 20 2012 - 05:43:18 CDT

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).

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