[gmx-users] MD structure analysis

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 9 17:23:55 CET 2011

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.


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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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