[gmx-users] g_rms with two trajectories

[Erik Marklund]

Dear Julian,

I see no other means than writing a script to parse out the diagonal. The xpm format is quite human readable so I don’t think it will take you long to figure out how to do.

Kind regards,
Erik

On 9 Feb 2015, at 14:16, Julian <julimoxx at gmail.com<mailto:julimoxx at gmail.com>> wrote:

Dear Erik,

I have the matrix and I converted it with xpm2ps into a coloured image.

I want to compare the ligands at the "same time"  so I would be interested
in the diagonal.

Which is the best way to get from the xpm matrix the diagonal plotted in 2d
as a function of time and rmsd value?

Best regards,
Julian

Message: 5
Date: Mon, 9 Feb 2015 12:28:04 +0000
From: Erik Marklund <erik.marklund at chem.ox.ac.uk<mailto:erik.marklund at chem.ox.ac.uk>>
To: "gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>" <gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>
Subject: Re: [gmx-users] g_rms with two trajectories
Message-ID: <B783245E-BBC6-45DD-908F-CD21B2DA3F80 at chem.ox.ac.uk<mailto:B783245E-BBC6-45DD-908F-CD21B2DA3F80 at chem.ox.ac.uk>>
Content-Type: text/plain; charset="us-ascii"

Dear Julian,

Use the -m flag.

Kind regards,
Erik


Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

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

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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