[gmx-users] RMSD of the same protein in different solvent boxes

Ran Friedman r.friedman at bioc.unizh.ch
Mon Feb 5 11:22:55 CET 2007


If it's the same protein you can extract the trajectories with the
coordinates of the protein only using trjconv.


Afonso Duarte wrote:
> Hi to All,
> I have some simulations of the same protein in different solvents,
> with different number of atoms for each (different solvent number of
> atoms).
> I would like to calculate a rmsd matrix to compar the backbone of the
> different sims.
> I have tried g_rms with the -f2 option to include the second
> trajectory, however it finishes with a fatal error because teh number
> of total atoms is different in both trajectories.
> Does anybody know how to solve this question? Is it possible to
> produce the rmsd matrix in a different way?
> Thanks in advance
> Afonso
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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