[gmx-users] how to obtain error bar for plotting?

[Mark Abraham]

On 28/12/11, leila karami <karami.leila1 at gmail.com> wrote:

> Dear Mark
> 
> 
> can I obtain error bar twice the standard error of the average

 
If you've used g_energy -av on multiple sets of data, then it will plot error bars corresponding to various quantities. Since twice the standard error isn't an option it supports (as you know from reading g_energy -h) then you'll have the option of accepting one it does support or looking at the output file with error bars of (say) one standard error and post-processing to double the size.
 

> 
> distance between the donor atom of protein and acceptor atom of dna over 1 simulation?

 
You've made one observation from one simulation, so there is no statistical error to report. 
 

> 
> 
> should I do several simulation. Is 1 simulation enough?

 
Very likely you should do several simulations each much longer than 1ns. You should also examine the literature for people who've tried to observe similar things on similar systems to use their approach as a guide for your own. 
 
Mark 

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