[gmx-users] g_rmsf calculation

[Justin A. Lemkul]

Moutusi Manna wrote:
> 
> Dear all,
>            how can i calculate the root-mean-square fluctuation 
> (RMSF)(last 5ns) of a group of atoms relative to their equilibrium position?
>            the command i have used  is
> g_rmsf -f mer.xtc -s md_1ns.tpr -n group.ndx -o rmsf.xvg -nice 4 -b 
> 35000 -e 36000
> where, md_1ns.tpr is the starting tpr for the production run.
> Is this one correct? if not please suggest me the command for rmsf 
> calculation after fitting to a referencee frame?

It is not correct for the question you are asking.  First, is the structure in 
the .tpr file the equilibrium structure?  Generally, the beginning of the 
simulation is not at equilibrium.  Second, using -b 35000 -e 36000 measures over 
only 1 ns, not 5.

> Again the output file is like.........(with 10 atoms in a group)
> ----------------------------------------------------------------------------
> # GRowing Old MAkes el Chrono Sweat
> #
> @    title "RMS fluctuation"
> @    xaxis  label "Atom"
> @    yaxis  label "(nm)"
> @TYPE xy
>     1   0.0993
>     2   0.0679
>     3   0.0468
>     4   0.1339
>     5   0.0680
>     6   0.0675
>     7   0.0141
>     8   0.1053
>     9   0.1004
>    10   0.0966
> --------------------------------------------------------------
> Can i get a single value for the whole group, except the rmsf values for 
> each atoms in the group?

No, but you can get these values averaged by residue with -res, although I think 
there is a pending bug report on the matter:

http://bugzilla.gromacs.org/show_bug.cgi?id=358

-Justin

> with regards,
> 
> Moutusi Manna
> 
> 
> 
> 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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