[gmx-users] RMSD value

Fitsiou, Eleni e.fitsiou at lancaster.ac.uk
Mon Oct 2 22:55:57 CEST 2017

Dear users,

I have a question regarding the calculation of RMSD value for a big system comprising of many replicas of the same peptide.
I know that with RMSD fit you can choose to “superimpose” your reference structure to the one from the trajectory (rot+trans). My question is when supplying gmx rms with -s the structure file (that has all the peptides) does it treat it as a whole object? should I supply with the s flag an em.tpr of a single peptide (and ignore the warning about mismatch of number of atoms?).
I am getting big values (nm) and trying to understand what I did wrong. I would like gmx rms to give the average value for displacement for all the peptides for each frame from the trajectory. 

Thank you in advance!

Best, Eleni   

More information about the gromacs.org_gmx-users mailing list