[gmx-users] g_rms with two trajectories

[Smith, Micholas D.]

Juilan,

A quick way to do this is with an awk script, such as:

awk '{print $NR}' (your matrix.dat file here). This will print the diagonal of the matrix. If you want the one from the .xpm file you need to use something like:

awk '{if($0!~/*/){print substr($0,counter+2,1),counter++}}' Though the output will be letters that correspond to different rmsd values (as shown at the top of the .xpm file) which will require you to modify this script more to include a look-up to get back the number values (hence why using the matrix.dat file may be easier).


Kind Regards,

Micholas


===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Julian <julimoxx at gmail.com>
Sent: Monday, February 09, 2015 9:16 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] g_rms with two trajectories

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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