pawan raghav wrote:
Dear Justin,
Thanks for sharing your knowledge with me. I have gone through
the tutorial and observed -extrn extract projected structure along with
first two eigen vectors. Each Eigen Vector represents minimum and
maximum strucuture value.
I am a bit confiused about the values for minimum and maximum. I dont
know the exact meaning of score for minmum and maximum values. Are these
values
deviation (Displacement) and what is its unit and which score is the
best score along any eigen vector?
Please help me out with this problem. Is it possible to extract minimum
energy sructructue from a MD trajectory by using G_anaeig. Give me some
clue about these minimum/maximum scores.Can i consider thhis mimimum or
maximum structure as a native structure?
I thought this looked familiar. You asked this question before:
http://lists.gromacs.org/pipermail/gmx-users/2010-August/053511.html
and received an answer with a very nice analogy:
http://lists.gromacs.org/pipermail/gmx-users/2010-August/053517.html
I don't think there is any relationship in the maxima/minima to native
structures. If I recall, the extremes are based on an average structure, which
may or may not actually have any physical relevance:
http://www.gromacs.org/Documentation/Terminology/Average_Structure
I doubt that g_anaeig is appropriate for determining any sort of minimum energy
structure, but I have not used it extensively to know for sure.
-Justin
Pawan Raghav
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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