you can make a simple script which calculates all the pairwise RMSD
values with g_rms. By doing this you can make a "RMSD matrix".
The usefulness of this depends on what you are trying to see, which
wasn't clearly stated to us. I did it once because I wanted to know how
similar the 20 conformers from a NMR PDB actually were.
2013/1/24 FLOR MARTINI <flormart...@yahoo.com.ar>
> The values are OK, you obtain a value of RMSD of 0.2510229 . The value -1
> refers time, and it is because you do not have a trajectory. You are
> comparing only two .pdb structures, so it is consistent that you obtain
> only one value, as you do not have more than one frame to compare.
> Regards
> Flor
>
> Dra.M.Florencia Martini
> Cátedra de Farmacotecnia II
> Facultad de Farmacia y Bioquímica
> Universidad de Buenos Aires
> Junín 956 6º (1113)
> TE: 54 011 4964-8273
>
>
> ________________________________
> De: Shima Arasteh <shima_arasteh2...@yahoo.com>
> Para: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Enviado: miércoles, 23 de enero de 2013 16:14
> Asunto: Re: [gmx-users] RMSD
>
> What I see in xvg file is as below:
>
> # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
> #
> # g_rms is part of G R O M A C S:
> #
> # Gromacs Runs On Most of All Computer Systems
> #
> @ title "RMSD"
> @ xaxis label "Time (ps)"
> @ yaxis label "RMSD (nm)"
> @TYPE xy
> @ subtitle "Protein after lsq fit to Protein"
> -1.0000000 0.2510229
>
>
> I though that -1 is the ref value and the other is the relative RMSD for
> 2.pdb. Is this -1 should be positive? What is this -1? Would you give me
> any suggestions please?
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Justin Lemkul <jalem...@vt.edu>
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Cc:
> Sent: Wednesday, January 23, 2013 9:36 PM
> Subject: Re: [gmx-users] RMSD
>
>
>
> On 1/23/13 12:48 PM, Shima Arasteh wrote:
> > I want to find the structure with the lowest RMSD, so I think it does
> not make different to set any of pdb files as the ref structure.
> > I made an attempt and got the RMSD regarding the first pdb file. The
> RMSD relative to -1 for the ref structure, is written in xvg file. Is my
> approach logically correct?
> >
>
> The RMSD value should be positive, so I don't know how you get -1. Your
> approach does not seem very sound - a structure does not have an absolute
> RMSD value; it has an RMSD value relative to a reference structure, which
> must be some sort of meaningful comparison or else you're not really
> measuring anything useful.
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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