Is it better to align all the trajectory before calculating rmsd?

From: dongsheng lei (laidongshengs_at_gmail.com)
Date: Tue Jan 22 2008 - 03:05:47 CST

Hello!

In some paper about simulating protein with namd, I find they verify the
equilibration of protein by the root mean square deviation (RMSD).But they
don't align all the trajectory before calculating rmsd.
Is it better to align the entire trajectory to the initial structure before
calculating the rmsd, for rmsd may be derived from translation and
rotation?
Are there some other methods to verify the equilibration of protein?

Thank you very much!!

Best wishes

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