[gmx-users] Distance travelled from time 0

Parker de Waal Parker.deWaal09 at kzoo.edu
Thu Jun 20 14:44:51 CEST 2013

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

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:


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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