jalemkul at vt.edu
Wed Jan 23 19:17:18 CET 2013
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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