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
--
========================================
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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