Dechang Li wrote: >>>>> In the 16 CPUs simulation, the RMSD of protein at t=0 was about >>>>> 0.1 nm, why not equal to zero? I used the initial structure for the >>>>> least squares fit. >>>> If you've done an equilibration or EM, the structure can have changed >>>> during that. >>> I mean the initial structure is the structure I used to generate the >>> .tpr file for mdrun_mpi. >> What were your command lines, choices for groups and outputs? The most >> likely simple explanation is that you haven't done what you think you've >> done :-) > > My command lines: > > g_rms -s md.tpr -f md.trr -o rms_protein.xvg -n index.ndx > > choices for groups: > > Select group for least squares fit: Protein > Select group for RMSD calculation: Protein
Have you used gmxcheck to see if the coordinates in md.tpr match the first frame of md.trr? If you're using constraints then these are probably applied before writing the t=0 md.trr frame, check that. You have managed to avoid one common mistake, which would be to use a .gro or .pdb file as input to -s, and not to realise that these are reduced-precision file formats and thus differences from rounding errors are to be expected. 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
