[gmx-users] RMSD

[FLOR MARTINI]

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_arasteh2001 at yahoo.com>
Para: Discussion list for GROMACS users <gmx-users at 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 <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at 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

========================================
-- gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists