[gmx-users] RMSD output from gmx confrms differs from gmx rms?

[Susan Khor]

Hello:

I would like to measure the C RMSDs between structures from a
trajectory and a PDB structure.
With gmx rms, I get warning messages about different number of atoms
in the input files.

So I create pdb files from the trajectory, with solvent excluded.
But when I run gmx confrms with these pdb files, I get different RMSD values.

Which is the correct way to do this?

Also how do I output the RMSD result from gmx confrms - it's just the
one line at the end of the output, which I'm now collecting in a file
and then doing a grep.

Thanks,
Susan