[gmx-users] MD structure analysis

[Justin A. Lemkul]

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

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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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