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

David van der Spoel spoel at xray.bmc.uu.se
Mon Dec 16 16:00:00 CET 2002

On Mon, 2002-12-16 at 10:14, Marc Baaden wrote:
> Hi,
> Short version: when calculating an rmsd matrix for a protein
> trajectory, how many frames should one take into account (eg
> skip 5ps or 10ps of the saved frames ?)
> Longer version:
> This is more an application or rule-of-thump like question.
> I was about to calculate an rmsd matrix for a 10 ns trajectory
> with 1 frame per ps, eg 10000 frames.
> For one this would take quite a while to build the 10k x 10k
> matrix, and for two, I think that it would bring in more noise
> than information.
> Eg, as motion in nearby frames is most probably correlated,
> structures will be quite similar, and doing the matrix for
> those frames would just show the similarity of those nearby
> frames, which is not what I want.
> I am rather interested in how close/similar uncorrelated
> frames are.
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
323 (1): 153-164 OCT 11 2002

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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