**From:** Ajasja Ljubetič (*ajasja.ljubetic_at_gmail.com*)

**Date:** Thu Jun 26 2014 - 08:05:48 CDT

**Next message:**Ivan Gregoretti: "Re: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation??"**Previous message:**Shailesh Pandey: "Re: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation??"**In reply to:**Giacomo Fiorin: "Re: PMF and work distribution"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

There are also a lot of normality tests

<http://en.wikipedia.org/wiki/Normality_test> Such as Anderson-Darling

<http://en.wikipedia.org/wiki/Anderson%E2%80%93Darling_test>, Shapiro-Wilk

<http://en.wikipedia.org/wiki/Shapiro%E2%80%93Wilk_test>, etc.. Be advised

that these only work well for small sample sizes (less than ~500-1000

samples). If very large samples are used the tests always reject

<http://stats.stackexchange.com/questions/2492/is-normality-testing-essentially-useless>

the distribution. The solution I've used in the past is just to randomly

draw 500 samples from my original huge sample set.

There are also Q-Q plots

<http://en.wikipedia.org/wiki/Quantile-quantile_plot> for graphically

determining deviation from normality (or in general the deviation of two

probability distributions).

Best regards,

Ajasja

On 25 June 2014 19:12, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:

*> Hello Mustafa, there are a multitude of recipes and opinions on this.
*

*> Generally, you would simply calculate the 3rd and 4th statistical moments
*

*> of the distribution, comparing them to those of the normal one (Gaussian).
*

*>
*

*> Giacomo
*

*>
*

*>
*

*> On Wed, Jun 25, 2014 at 6:50 AM, Mustafa Tekpinar <tekpinar_at_buffalo.edu>
*

*> wrote:
*

*>
*

*>> Hi,
*

*>> I am performing SMD simulations and I want to calculate Potential of Mean
*

*>> Force (PMF) using those simulations. As far as I know, work distribution
*

*>> (or force distribution) has to be gaussian to calculate PMF (with
*

*>> Jarzynski's method and second order cumulant expansion). I was wondering
*

*>> how can I check if my work distribution is gaussian.
*

*>>
*

*>> Thanks in advance,
*

*>> Mustafa Tekpinar
*

*>>
*

*>
*

*>
*

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