[gmx-users] RMSF reference state?

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 13 23:57:23 CEST 2009

Pan Wu wrote:
> Hi everyone,
>     Thank you for answering my former questions, it really help me, the 
> new gmx-er a lot~
>     Here is another question about reference state of RMSF.
>     In the manual, it shows "g_rmsf computes the root mean square 
> fluctuation (RMSF, i.e. standard deviation) of atomic positions 
> after (optionally) fitting to a reference frame". So in this way, can I 
> choose the reference frame from *.tpr file or the coordinate average 
> over the whole trajectory? If Gromacs can, how?

I believe the reference structure is taken from whatever structure file is given 
to the -s flag, so in principle you could provide any frame from the trajectory, 
as well as the initial one, or some average structure (from, i.e. g_cluster or 
something similar).


>     Thank you  in advance!
> -- 
> Sincerely
> =================================
> Pan Wu
> Graduate Student in Department of Chemistry
> Duke University
> 124 Science Drive
> 5301 French Family Science Center
> Durham, NC 27708
> Phone: (919) 660-1583
> =================================
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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