Re: RMSD calculation

From: Mert Gür (
Date: Fri Aug 02 2013 - 22:22:35 CDT

Sure. Simply load the pdb structure as a (second) new molecule. So now this
is your "top" molecule. When you calculate the RMSD you will use that as
your reference structure.
Please let me know if you need a more detailed description.
On Aug 2, 2013 9:46 PM, "Vibhor Agrawal" <> wrote:

> Dear Namd Users
> I have a small doubt the way RMSD calculation are done in NAMD.
> i have a trajectory of 783 frames and when I try to calculate the RMSD
> ,Calculations are based on the first frame as a reference. Is it possible
> to calculate the RMSD based with the pdb structures as a reference.
> Thanks
> Vibhor

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