[gmx-users] Why should I repeat my simulation?
jalemkul at vt.edu
Sun Oct 5 04:18:07 CEST 2014
On 10/4/14 5:15 PM, fatemeh ramezani wrote:
> Dear gmx-users
> I performed a MD simulation with gromacs software and after sending my results to a journal, referee said
> "Simulations needs to
> be repeated with different initial velocity (seed) to make sure that the
> results are not simulation artifacts.It is needed to ensure that the simulation represents true dynamics
> of the system."
> It is really need to I repeat my simulation (that is very time-consuming process) or you can help me to providea compelling reason for not repeating.
The reviewer is right. A single simulation is generally insufficient to provide
convincing evidence of any behavior, unless it is exceptionally long and shows,
for instance, reversible behavior. In reality, no simulation is probably ever
truly converged. That is why it is standard practice to conduct multiple
simulations, exactly as the reviewer says. One would never perform a single
biological assay and claim it to be exactly correct, why should one simulation
be the exact answer? Perhaps your one simulation would end up being the outlier
in a data set.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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