[gmx-users] g_rms with two trajectories

Erik Marklund erik.marklund at chem.ox.ac.uk
Mon Feb 9 13:28:08 CET 2015

Dear Julian,

Use the -m flag.

Kind regards,

Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

On 9 Feb 2015, at 12:20, Julian <julimoxx at gmail.com<mailto:julimoxx at gmail.com>> wrote:

Dear Gromacs Users,

I want to calculate the rmsd between two ligands - the system is exactly
the same, just the ligand binding conformations are different.

Therefore i want to use g_rms with the option -f2 as in the following

g_rms -f trajout.trr -f2 ../2/trajout.trr  -n -o

In g_rms -h it says that this "generates a comparison matrix of one
trajectory versus the other" but I don't get this matrix.
Only the "normal" rmsd.xvg but it seems as it is calculated to the starting
snapshot and the f2-trajectory file is not considered.

Could anyone explain me how I execute this command correctly?

Thanks and best regards!
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