Thanks for your valuable suggestions. I am totally agree with your views. On Fri, Apr 6, 2012 at 00:11, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > bipin singh 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. >> > > No one can do anything for an infinite amount of time ;) Hence replicate > simulations and thorough statistical analysis are required to obtain > reliable results and prove that what you've done is to be trusted. The > other comments in this thread are quite good so I won't recapitulate other > points that have been made. > > > And also how to believe the statement made by several research papers >> based on unconverged simulations. >> >> > I wouldn't trust any conclusions drawn from demonstrably unconverged > simulations. Not everything that's published has been done correctly. > Peer review is an imperfect system, so be careful what you read and apply > good scientific judgment. > > -Justin > > On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul <jalem...@vt.edu <mailto: >> 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<http://www.gromacs.org/__Documentation/Terminology/__Reproducibility> >> >> <http://www.gromacs.org/**Documentation/Terminology/**Reproducibility<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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >> ==============================**__========== >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> ----------------------- >> /Regards,/ >> Bipin Singh >> >> > -- > ==============================**========== > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- ----------------------- *Regards,* Bipin Singh
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