[gmx-users] RMSD

[Justin Lemkul]

On 1/23/13 1:14 PM, Shima Arasteh wrote:
> 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?
>

That is the value of time, normally read from a trajectory.  Please note that 
the "xaxis" label tells you this.  When no value is found (i.e. when comparing 
one structure to another, not part of a trajectory) there is no time value and 
thus g_rms prints -1.

-Justin

-- 
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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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