[gmx-users] resolution influence on simulations

[K.A. Feenstra]

Ruben Martinez Buey wrote:
> Hi everybody,
> Thanks a lot for your help.
> Anyway, the lower is the resolution, the more is the r.m.s deviation 
> after the run??
> I mean you can use a cut-off to check which changes are really 
> significatives [r.m.s.d Vs residue number], and this cut-off can be the 
> r.m.s.d of the last step in the simulation plus the averaged r.m.s.d. of 
> all the residue`s rmsd at the end of the run. Is it right??

Weeellll..., it isn't quite that straightforward.

First off, it depends on what you want to look at. Taking e.g. Lysozyme
as an example, its large two-domain hinge-opening/closing motion gives
rise to relatively large RMSD's. If you have only a small helix or loop
moving, e.g. to cover the active site, RMSD's can be much lower.

Relating RMSD's to number of residues is a good thing, though. 0.2 nm
RMSD on a 10 residue peptide isn't the same as on a 100 residue protein!
There is a paper on it by Majorov & Crippen:

Maiorov, V. N., Crippen, G. M. "Size-independent comparison of protein
three-dimensional structures." Proteins: Struct. Funct. Gen. 22:273-283, 1995.

where they derive a size-independent version of RMSD, they call 'rho_sc'.
Sadly, it is more complicated to calculate than RMSD, meaning it will
most probably not catch on... It *is* implemented in g_rms, though.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
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