[gmx-users] results of md

mohammad agha mra_bu at yahoo.com
Tue Dec 4 22:15:04 CET 2012

Dear Justin,

Thank you very much from your response.
It means that this problem is not important. Should I use -reprod option in running of md.mdp? I want to obtain micelles as monodisperse with identical Nagg(aggregation number) in the one simulation, but distribution of sizes is broad and it is opposite of experimental results. 
Can you help me about this problem, Please?

Best Regards

----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, December 5, 2012 12:31 AM
Subject: Re: [gmx-users] results of md

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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