[gmx-users] g_rms -prev option .. strange behaviour

Marc Baaden baaden at smplinux.de
Wed Aug 7 18:40:43 CEST 2002


I wanted to compare 2 trajectories of different but comparable systems.
So I put them both (restricting to C-alphas) in a same trajectory and
catted them together with trjcat. Analysis with g_rms -prev (offset)
yields a strange result ..

.. so I thought let's do a blank, and just cat the same trajectory
twice. That should yield a constant RMSD of 0 as it is the same
trajectory. Funnily enough that is not the case ! So if anybody has
a suggestion .. you can quite easily reproduce it with any short
trajectory you have. I did something like

trjcat -settime -o double.xtc my.xtc my.xtc

and eg choosing 'c' for the times. Assuming that the trajectory was
500 ps long and frames were written out every 10 ps, then

g_rms -o -b 500 -prev 50 -s my.pdb -f my.xtc 

should start at the second half and compare to the first half.
Inspection of rmsd.xvg doesn't show the expected flat 0 line ..

Did I try something stupid ?


 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
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