> trajin pdb_wat_md1.mdcrd
> trajin pdb_wat_md2.mdcrd
> rms first out pdb_wat.rms time 0.2
If you read the output from CPPTRAJ (or ptraj) it will show you that you
selected all atoms for the rms command (i.e. all waters + biomolecules).
This will be a large RMSD. To select a subset, select some atom mask:
rms first mass out pdb_wat_P.rms .P time 0.2
If you need more information on masks, read the CPPTRAJ manual.
--tec3
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Received on Tue Sep 22 2015 - 14:00:06 PDT
