Dear Justin, Thank you very much for your reply and especially your time. According to my structural analysis my convergence sounds good as you mentioned, my diffusion coefficients, RDF, number density profiles over different time intervals show stable states.
Ali Alizadeh Justin wrote: Neither temperature nor total energy tells you anything about convergence. They are related instead to the stability of the various algorithms employed during the simulation. In fact, one can manipulate these quantities rather easily by tweaking settings inappropriately. Convergence is more rigorously assessed through physical observables in your system. For a simple fluid, do its properties (density, diffusion constant, RDF) change over different intervals of simulation time? If they do, the simulation isn't converged. For biomolecules, looking at any number of structural properties can be informative. By your criteria above, my multi-domain heterodimeric protein complex was converged after about 5 ns. In reality, it underwent large, cyclical transitions over the course of 500 ns. -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 jalemkul at outerbanks.umaryland.edu <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> | (410) 706-7441http://mackerell.umaryland.edu/~jalemkul On Tue, Aug 19, 2014 at 7:00 PM, Ali Alizadeh <ali.alizadehmoja...@gmail.com > wrote: > Dear All users, > I have been engaged in answering this question"how long should we continue > calculating to make sure we can get justifiable results?". Are there any > suggestions to dig out to find out when a system converges? I know this is > a too general question. > In case of my systems(confined structure, interface between fluid and > solid) after 1ns simulation my temperature fluctuation shows quite > convergence, my total energy corroborates this convergence too. > > > -- > Sincerely > > Ali Alizadeh > -- Sincerely Ali Alizadeh -- 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.