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 -- ================================================== 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.
