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

[Ewaru]

Hi Justin,

Thank you for your prompt reply! As this is my first approach to molecular
dynamics, I still have lots of to understand but I'm constantly reading and
trying to work things out. I predicted 2 structures, one using Modeller, and
another one with I-Tasser. I followed your very informative tutorial for the
approach of energy minimization and equilibration using Gromacs. My mistake
for assuming that RMSD should fall within 0.1nm. I'm supposed to choose the
best model to proceed with docking. Is it okay if I run just a 10ns
simulation for both the predicted structure and then decide the best one by
comparing the stability of the protein, from the output of the RMSD and
radius of gyration?

Thank you in advance.

Best wishes





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