[gmx-users] g_rms with two trajectories

[Julian]

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>
> To: "gmx-users at gromacs.org" <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>
> 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>> 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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