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 <deviceran...@gmail.com> wrote: > On 5 Oct 2014 04:18, "Justin Lemkul" <jalem...@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 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > ================================================== > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.