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

[João M. Damas]

Some care must be taken with the use of the term "replica", due to the
amount of replica-exchange schemes around. The "replicate simulations"
being talked about here do not imply exchange schemes and different
hamiltonians. Just to make things clearer.

João

On Sun, Oct 5, 2014 at 4:15 PM, massimo sandal <devicerandom at gmail.com>
wrote:

> 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.
>
> > --
> > ==================================================
> >
> > 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
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613