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

[Florian Haberl]

Hi,

On Wednesday, 23. May 2007 10:04, 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.


use the tool g_covar to generate average structure with -b and -e you can 
chose start and end point of the calculated average structure.

If you want average running structures you can move the window of the 
calculated structure forward.


Greetings,


Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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