[gmx-users] Why should I repeat my simulation?

[massimo sandal]

On 5 Oct 2014 04:18, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>
> 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
>

Agree with Justin. At least three replicas should be done. Note also that
comparing different simulations can tell you more interesting things about
your system. It's always not only necessary but enriching.

M.

> --
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> 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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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