[gmx-users] Bug in g_rms -> calculate RhoSc ??

[Marc Baaden]

>>> "K.A. Feenstra" said:
 >> > Did you look at MArc's figures? It seemed like PBC errors to me... Or
 >> > maybe lsq fitting errors.
 >> 
 >> What type of system is this? Maybe a di-(or multi-)mer across the box
 >> edge could do this? Marc, could you also put up the normal rms figure?

Hi,

it's a beta-barrel protein, I included a picture of the Calpha trace -
which is what I was analysing - at

http://indigo1.biop.ox.ac.uk/mbtemp/barrel.png

As you can see, it is a monomer.
The normal rmsd is at

http://indigo1.biop.ox.ac.uk/mbtemp/rmsd.png

it is least-squares fitted to a selection of Calphas which show dominant
secondary structure for most of the trajectory.

I should maybe point out that I get the same kind of weird
rhosc plot for a number of other systems.

Marc
-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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