[gmx-users] rmsf question

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 16 10:50:56 CET 2010

Hi Andrei,

> If I correctly uderstand the RMSF computed on C-alpha in PDB NMR
> structure, is a measure of the uncertanty in resolving the structure.

No, that's not what I said. You're saying that there's one structure
(the structure), but there is uncertainty in resolving it. That's not
the case. There is a distribution of structures that gives rise to a
set of signals, from which time and ensemble averaged distances
between certain pairs of atoms can be deduced. But this set of
distances is typically leaves a number of degrees of freedom, and on
top of that the time averaging may actually yield restraints that
cannot be satisfied simultaneously. So, structures have to be fit to
the set of distances, which is typically repeated a large number of
times using simulated annealing with different starting conditions.
>From the resulting set the ones best fitting the data are selected and
put forward as a representative set of structures. The least defined
regions, in terms of (distance) restraints are likely to show most
variation. But the structures are not weighted according to their
probabilities and therefore neither the average nor the fluctuations
can be expected to coincide with the moments of the Boltzmann

> Compared to this the RMSF of C-alpha computed from a MD trajectory
> reflects the geometric fluctuations of the backbone in the Boltzmann
> distribution of states in the generated ensemble.

Assuming you have sampled long enough and not just trying to explain
drift as fluctuation :)

> The uncertanty in the NMR structure can be influenced by the thermal
> fluctuations in the backbone geometry.

Well, that's part of it, but the way the models are derived contributes a lot.

> Only in this respect the comparison of the two makes sense.
> Is this correct?

Comparisons can be made, but you have to formulate and justify your assumptions.



Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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