Re: RMSD trajectory

From: Nikolaos Glykos (
Date: Fri Nov 18 2011 - 14:32:41 CST

 This is possibly a question for the VMD list (?).
 "RMSD-trajectory" is rmsd from the starting (or a reference) structure
 ? Or
 something else ?

 In any case, the answer is that probably doesn't matter as long as the
 (or PSF) has the right atoms in the right order (identical with the one
 in the DCD file).

 On Fri, 18 Nov 2011 12:09:15 -0800 (PST), flavio seixas wrote:
> Hi all.
> My question is: What is the best choice to calculate RMSD-trajectory
> plot for a simulation?
> The psf file plus the dcd file or the pdb file plus the dcd file?
> Or does not matter?
> Regards,
> Flavio

             Nicholas M. Glykos, Department of Molecular Biology
      and Genetics, Democritus University of Thrace, University Campus,
   Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) 
     Ext.77620, Tel (lab) +302551030615,

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