[gmx-users] probability distribution of bond distance/length

Mark Abraham mark.j.abraham at gmail.com
Fri Nov 1 10:25:58 CET 2013


On Fri, Nov 1, 2013 at 4:04 AM, Xu Dong Huang <xudonghmath at gmail.com> wrote:

> Dear all,
>
> I would like to assess the probability distribution of particle bond
> distance/length over the entire run, specifically I want to collect
> possibly a histogram representation or even a regular plot. Would using
> g_bond be the correct way to obtain the probability distribution?


g_bond -h and/or manual chapter 8 are the best places to start.


> Or is there another function that gets probability distribution
> specifically. Also, if using g_bond, it will give me an average (I
> suppose), so how can I get a histogram/data series representation? (I do
> not want to visualize this result using xmgrace)
>

g_analyze, or your favourite maths/stats software package.

P.S I believe someone earlier suggested a link to the data collection
> reporting procedure, I tried it and changed the .xvg to a .csv, but the
> data reported in excel format all belongs to 1 single column, which won’t
> let me make a plot.
>

A plot of two columns, no, but it should let you plot a histogram!

Mark



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