Dear all, I would like to have some elucidation about g_rmsdist output. Optionally, it outputs three matrices with the options -rms, -mean and - scl. Questions are:
1) Exploring .xpm files, I see there is a letter code which converts color exa-codes to letters to values. The "resolution" is tunable with option -nlevels, but the range is delimited by the highest calculated value. Is there a way to assign a fixed range (in order, e.g., to compare different trajectories of the same protein)? 2) -rms output, I guess, is the deviation from average distance, over time, for each atom couple. I see my matrix is full of 0's. I expected 0's on the principal diagonal (distance of an atom from itself is obviously always zero), but others? It should mean atoms' distances RMSD are 0, that is they do not deviate... but they don't look that fixed at all from the trajectory! This is even more surprisingly in the -mean output, which should contain, I guess, atom distances averaged over time. In that case there are lots of 0's too. Maybe my "I guess" are wrong... 3) What is, actually, -scl output? Thanks in advance to anybody who will answer. Fabrizio _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
