[gmx-users] results of md

Justin Lemkul jalemkul at vt.edu
Tue Dec 4 22:01:25 CET 2012

On 12/4/12 3:57 PM, mohammad agha wrote:
> Dear Gromacs Specialists,
> I ran one system (to create of micelles) tow times. Time of creation of micelles was different in each run and for example if it has been created 5 micelles (in the end of simulation) in both of them but the number of molecules presence in micelles (aggregation number) is different.
> My question is that why the results of systems aren't identical?
> May I ask you to answer my question, Please?

Simulations rarely are identical and hence why extensive sampling is important. 
  Think about micelle formation under experimental conditions.  How long does it 
take?  Seconds?  Minutes?  I am willing to bet your simulations are orders of 
magnitude shorter, by necessity.  Simulation time and number of simulations 
(replicates) are important in deriving proper statistics, but there is certainly 
no guarantee that two simulations will ever be exactly the same. 
Reproducibility is discussed very nicely on the Gromacs website.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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