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 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 listgmx-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 listgmx-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 listgmx-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
