[gmx-users] how to find out the average running structure

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 23 10:12:04 CEST 2007

Sonali wrote:
> Hi everybody,
> i am a new user of gromacs, i had run simulation for 10,00000 iterations 
> with the protein 1f9b and have obtained all the required output files.
> after comparing and analysing the potential energy.xvg file and rms(root 
> mean square deviation).xvg file i have found out that there is most 
> minimal fluctuation between 1870 to 1926 ps region in both cases . now i 
> want to know how to find out the average running structure between these 
> regions. please suggest me how to obtain an average running structure 
> between 1870 and 1926.

I don't know, but if you check out manual section 7.4 and then the 
sections for the utilities that sound promising, you can probably do 
something like what you want.


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