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

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed May 23 10:15:02 CEST 2007


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.



 Florian Haberl                        
 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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