[gmx-users] Distance travelled from time 0

[Tsjerk Wassenaar]

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.deWaal09 at 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.stephenson at 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
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-- 
Tsjerk A. Wassenaar, Ph.D.