That's an interesting philosophical question. In this case, you'll wind up with a 50 ns trajectory where each configuration is consistent with the thermodynamic ensemble you're approximating. That's as close a definition to "realistic" as I think is worth worrying about. You'd only need to worry about mdrun not giving you exactly reproducible trajectories to 7 or 8 significant figures of precision in atomic coordinates if, simultaneously, nature behaved completely deterministically, you could observe a molecular system with that degree of precision, and your forcefield was exact; none of those three things are true.
That said, 50 ns seems like a very short time to simulate a complex system like protein/DNA/RNA. I'd be very worried about drawing anything other than observations from such a small data set (because you're almost certainly not converged in your sampling, as you allude to in your final question). MZ On Thu, Apr 5, 2012 at 2:08 PM, bipin singh <bipinel...@gmail.com> wrote: > Thanks for the reply. > I read the link. So, how one can predict something reliable using these > results(based on 50ns in my case) which changes on different machines? > which depends more on the environment of the computer architecture and other > variables of mdrun rather than system (Protein/DNA/RNA) itself for a short > simulation, where we don't have enough resources to run infinitely long > simulation. > And also how to believe the statement made by several research papers based > on unconverged simulations. > > On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul <jalem...@vt.edu> wrote: >> >> >> >> bipin singh wrote: >>> >>> Hi all, >>> >>> I am really surprised to see different results from two identical md >>> simulation. I have used identical tpr files for the mdrun (for 50ns) and >>> after the completion of the md job I found that the results from the >>> identical runs is totally different. >>> >>> To further confirm this, I have converted both the input tpr to mdp using >>> gmxdump and diff the two files and found that the mdp is identical. >>> >>> Please let me know what can be the reason of this behaviour. I know that >>> it is unexpected and even I can't believe how can it be possible. >>> >> >> It is not unexpected at all. Please consult: >> >> http://www.gromacs.org/Documentation/Terminology/Reproducibility >> >> -Justin >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > ----------------------- > Regards, > Bipin Singh > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
