[gmx-users] How much data to choose eg for an rmsd matrix

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 17 11:07:43 CET 2002

On Mon, 2002-12-16 at 15:22, Marc Baaden wrote:
> spoel at xray.bmc.uu.se said:
> >> Maybe it is more interesting to do the whole thing for average
> >> coordinates, take e.g. 100 average structures over 100 ps each, make
> >> them into a trajectory and compare those. Guaranteed lower RMSD, but
> >> probably also physically more relevant, see e.g.
> >> Native-like mean structure in the unfolded ensemble of small proteins
> >> Zagrovic B, Snow CD, Khaliq S, Shirts MR, Pande VS JOURNAL OF
> >> MOLECULAR BIOLOGY 323 (1): 153-164 OCT 11 2002 
> thanks for the reference, David. Looks very interesting, although I
> don't have 800 microseconds of data (*envy*). It is certainly an
> analysis idea that I will keep up.
Their simulations are without solvent, though it is still impressive.

> But considering my original question, I really want the standard/simple
> RMSD matrix, and only wondered how coarse I should/could get.
Since the RMSD usually don't change very fast, you can simply skip so
many as to cover your whle trajectory in a figure of reasonable size.
There are no rules here....

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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