[gmx-users] RMSD

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Jan 23 19:14:19 CET 2013

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?


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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