On 2/25/13 9:38 PM, Ewaru wrote:
Hi,
Just need some advice regarding the following results I obtained while
following the tutorial from this site, using a protein structure that I
modelled using Modeller.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
1. My output plot of RMSD doesn't converge. (From 0 - 0.4ns, its around
0.25nm, 0.4 - 0.7, around 0.3nm, 0.7 - 1.0ns, around 0.35). Does it mean
that my EM wasn't properly done? Anyway, the EM did not reach the requested
Fmax <100.
2. My graph for Radius of gyration from 800 - 1000ps shows a higher
fluctuation than the ones from 0 - 800ps. Does it mean that the structure is
not that stable?
Please advice. (I followed exactly the steps in that tutorial. I'm new to
Gromacs.) And of course, I neutralized my protein according to the charge
needed. Not exactly following blindly from the tutorial. ;)
Please don't assume that 1 ns of MD for any system is actually meaningful, or
that the results of some other protein will necessarily look anything like my
example. The commands in the tutorial are just to show how one might go about
doing analysis and demonstrating a few tools that can be used. Most protein
systems require tens, if not hundreds, of ns to manifest the behavior of
interest. The results you've posted indicate nothing more than the fact that
your protein isn't yet anywhere close to equilibrium, which is not at all
unexpected.
-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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