[gmx-users] g_rmsf calculation

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Nov 6 13:18:03 CET 2009


> 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.

Well, there is no physical equilibrium structure at all. Only an
ensemble. I would interpret equilibrium position as mean position in a
defined conformational space, achieved by removing rotational and
translational degrees of freedom for all frames according to some
criterium (LSQ fit against a reference, usually). Now that's exactly
what g_rmsf does: calculating the mean square fluctuation about the
equilibrium position in the conformational space defined by fitting
all frames to the reference structure. It doesn't really matter
whether that structure has significant probability in the equilibrium

>> 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:

Yes, you can sum them. This is actually equal to the trace of the
covariance matrix obtained using the same time window and fitting
procedure, and is a measure of overall motility.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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