[gmx-users] g_rmsf

[Xavier Periole]

hugo verli wrote:

>Hi,
>
>is there any way to do a RMSF analysis (with g_rmsf or another program) as a
>function of both residue number and time? I observed a considerable
>fluctuation of this property along the trajectory and I think it would be
>interesting to analyze if these movements are or not periodic.
>
>Many thanks in advance,
>
>Hugo Verli.
>
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I don't think there is. An alternative would be to cut your simulation 
in peaces
and do the analysis on each part. But the danger is that you need a minimum
of sampling to get some reliable fluctuations.
Idealy the more simulation you have the more accurate the fluctuations are
suposed to be. So cutting in peaces is kind of strange you better try to 
test
the convergence by increasing the size of the simulation you analyse.
How long are your simulations ?

XAvier

-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: md.chem.rug.nl/~periole
   
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