[gmx-users] g_rmsf

hugo verli hugo at acd.ufrj.br
Fri Feb 6 17:27:01 CET 2004

Initially the simulations were 4.8ns long. But when I did something like your
suggestion, i.e. rmsf analysis of each 400ps I observed the effect of the
equilibration in some loops of the simulated protein, with a very high rmsf
(<0.8nm) in the first 4 ns that decrease considerably in the last 400ps
(<0.2nm). The radius of gyration also decrease in this first 3 or 4ns, and I
understand to means the equilibration of some loops suffering of crystal packing. 

The first thing I did was to increase the conformational sampling of the
simulation, going to 8.0ns. The average of this 4.8 - 8.0ns simulation has a
rmsf value more stable, always lower than 0.2nm.

But looking the simulation in windows of 400ps I observe some kind of periodic
movements, i.e. a loop that increase and decrase its rmsf value along the
simulation. This profile is not shown in the average file. Because of this
behaviour I thought it would be nice to make some .xpm matrix with the residue
number, the time and the rmsf value in color, as the third dimension. So the
frequency of the peaks could indicate the periodicity of the movement.

I don't know if I was able to make myself clear, but if don't, please, tell me.


> 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
> -- 
> ----------------------------------------------
>    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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