Hi, g_rmsf doesn't do distances. To answer the question, you can use g_rms with -fit none and a suitable index group. Does depend a bit on what you mean with distance. The distance traveled by a residue could well mean the average distance for all particles in the residue, which is what you'll get with g_rms.
Cheers, Tsjerk On Thu, Jun 20, 2013 at 2:44 PM, Parker de Waal <parker.dewaa...@kzoo.edu>wrote: > 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 < > natalie.stephen...@manchester.ac.uk> 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 gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
