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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
