andrea carotti wrote:
Hi,
You should be getting such a 2200x33 matrix. My guess is that the
command line or files that you're using are not what you think they
are :-)
my command line is
g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin
If you read g_rms -h like I suggested last time, you'll see that -f2 and
-s serve the same purpose with the former using a trajectory and the
latter a single structure. That document doesn't say what happens when
you use both... but the operation you're trying to do doesn't need both!
Note that the pdbs (traj and ref) have the same number of atoms (same
structure).
During the calculation i can see that it is creating the 2200x33 matrix,
but on the rmsd.xvg i find only two columns. From the xpm and dat files
i can't extract the matrix (i don't know) to a text file.
There's an option to g_rms that writes a text matrix for importing into
R. Look it up.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
