larif sofiene wrote:
Greeting
After finishing a M.D simulation an ensuring that equilibration of the
protein is done in its solvent cube according to RMS, potential energy
,temperature , pressure , radius of gyration ... etc what structure
should i use for analysis ? is it the average structure of some few last
nanoseconds of the simulation , OR the structure of the last frame in
simulation, and is there any special cases where one of the two cited
structures could insight more than the other ? ( for example : for
Hydrogen bonds is the average structure more suitable for analysis than
the last frame ? ...)
A single structure should not be used for analysis, and you will likely find
that an average structure has very little meaning.
http://www.gromacs.org/Documentation/Terminology/Average_Structure
You should measure the observables of interest based on the question posed prior
to running the simulation, then average these relevant data over the
equilibrated time period.
-Justin
--
========================================
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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