VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Feb 27 2007 - 05:51:47 CST

Dear Sabri,

I've used the rmsf option in VMD and compared it with the results
obtained with g_rmsf (gromacs). Correct me if I'm wrong, but what I've
seen so far is that the rmsf in VMD is not calculated using an average
structure, but the first frame of the trajectory (as in RMSD). Maybe
you could also try g_rmsf and compare your results.

Cheers,
Michel

2007/2/27, bora erdemli <boraerdemli_at_yahoo.com>:
> Dear VMD Users,
>
> I was trying to understand the options that measure
> rmsf command has.
>
> rmsf selection [first first] [last last] [step step]:
> Returns the root mean square position fluctuation for
> each selected atom in the selected frames. If no
> first, last, or step values are provided the
> calculation will be done for all frames
>
> what is this step option used for?
>
> In rmsf calculations,there is supposed to be a
> reference frame or an average structure that is taken
> as a reference.
>
> Do you have any idea about what the reference
> structure is? or is there anyway to specify it
> manually?
>
> thank you very much in advance
>
>
> Sabri Bora Erdemli
>
>
>
>
>
>
>
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