From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Jun 21 2006 - 10:10:08 CDT

Hello Arturas

I have had this same question/quandry. Most rmsf are calculated using a
reference structure that is not the starting/crystal structure rather the
reference structure is one that is calculated by averaging a number of
structures and then using that as a reference to get your fluctuations.

This is how the Daggett group rmsf's are calculated and it would seem to
be the case in gromacs.

Calculating rmsf's in this way they are not biased by the often large
change in rmsd from the starting/crystal structure which swamps the signal
so to speak.

I just need to spend some time writting a script that will do this
calculation in this manor.

  my .02

Brian

On Tue, 20 Jun 2006, John Stone wrote:

>
> Arturas,
> No, not like Gromacs. The 'measure rmsf' command assumes
> that you've alredy done the fitting (as with 'measure rmsd').
> No, the rmsf for each atom is calculated independently. If you want
> all atoms in a group, you'll want to use 'measure rmsd' and provide
> an appropriate group selection instead.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jun 20, 2006 at 08:33:32PM +0000, ziemys_at_ecr6.ohio-state.edu wrote:
>> HI,
>>
>> Is RMSF in VMD computed as in GROMACS (the root mean square standard deviation of atomic positions after first fitting to a reference frame) ?
>>
>> What frame is the reference for fitting (if RMSF calculated like in GROMACS) ?
>>
>> Will the average computed RMSF of all atoms in a residue be the same as a group RMSF ?
>>
>> With best
>> Arturas
>>
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

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