Hi Natalie, You might want to look into g_rmsf, used to calculate the root mean squared fluctuation of atoms or residues.
sample usage: g_rmsf -f trajectory.xtc -s struc_mass.tpr -oq rmsf.pdb -o rmsf.xvg Additional commands of interest: -res (when true, calculates residues as a whole) -b (first read frame) -e (last read frame) For more information see the guide: http://manual.gromacs.org/current/online/g_rmsf.html Cheers, Parker On Thu, Jun 20, 2013 at 5:50 AM, Natalie Stephenson < [email protected]> wrote: > > Hi guys, > > What is the best way of calculating how far a residue has traveled from > its starting position during a simulations? > > Thanks > Natalie > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
