[gmx-users] RMSD

[Michal Walczak]

Hi there!

How should I generate RMSD chart for protein. I put down the command:
g_rms -s input.tpr -f md_traj.xtc -o rmsd.xvg . My input tpr file was
the one which consist of *.top *.gro *.mdp files which I got from the
conversion the PDB file into gmx file (pdb2gmx). My second input
(md_traj.xtc) was the final trajectory file and when I started g_rms,
the group I chose was 'backbone' (no. 4). At last there occured
information that I violated (I don't know the proper word) memory
protection and I didn't get any output.

Best regards,

Michal Walczak