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

[Marc Baaden]

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.

But considering my original question, I really want the standard/simple
RMSD matrix, and only wondered how coarse I should/could get.

  Marc


-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
 FAX/Voice +49 697912 39550  -  Tel: +44 1865 275380  or  +33 609 843217