[gmx-users] Output for rmsd and radius of gyration doubts

Ewaru edina_wang at yahoo.com
Tue Feb 26 03:38:58 CET 2013


Just need some advice regarding the following results I obtained while
following the tutorial from this site, using a protein structure that I
modelled using Modeller.


1. My output plot of RMSD doesn't converge. (From 0 - 0.4ns, its around
0.25nm, 0.4 - 0.7, around 0.3nm, 0.7 - 1.0ns, around 0.35). Does it mean
that my EM wasn't properly done? Anyway, the EM did not reach the requested
Fmax <100.

2. My graph for Radius of gyration from 800 - 1000ps shows a higher
fluctuation than the ones from 0 - 800ps. Does it mean that the structure is
not that stable?

Please advice. (I followed exactly the steps in that tutorial. I'm new to
Gromacs.) And of course, I neutralized my protein according to the charge
needed. Not exactly following blindly from the tutorial. ;) 

Thank you very much in advance! :)

Best wishes. 

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