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

[Tsjerk Wassenaar]

Hi Sonali,

g_rmsf also gives average structures if you request so. It avoids the
covariance matrix construction/diagonalization g_covar does and will
save some time :)

Tsjerk

On 5/23/07, Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de> wrote:
> 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
>
> --
> -------------------------------------------------------------------------------
>  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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623