Re: automatic extraction of RMSD values of the heavy atoms of residues from NAMD output?

From: Maxim Belkin (
Date: Mon Aug 04 2014 - 11:25:15 CDT

Hi András,

This question is about post-processing the results of a simulation, so it is better suited for VMD mailing list.
Anyway, the webpage that you listed has an example of usage:
rmsd_residue_over_time top $sel resid FIRST_FRAME LAST_FRAME

So, you simply have to analyze NAMD trajectories one by one: load corresponding psf file in VMD (mol new filename.psf), make atom selections (set sel1 [atomselect top "..."], set sel2 ...), then load first trajectory (mol addfile trajectory.dcd waitfor all) and run rmsd analysis, repeat for the next trajectory, ...


On Aug 4, 2014, at 5:32 AM, Andras Borosy <> wrote:

> Dear all,
> As a beginner I may ask something very trivial again. I have my NAMD output files in a folder. I wish to extract of RMSD values of the heavy atoms of residues from all NAMD outputs automatically. I found some hints (like but I do not want to do it manually with many dozens of outputs.
> Best regards,
> Dr. András Péter Borosy
> Scientific Modelling Expert
> Fragrance Research
> Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf - Switzerland
> T:+41-44-824 2164 - F:+41-44-8242926 -

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