Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples 1 possible trajectory out of the ensemble of possible trajectories...
On 2012-04-05 11:38:20PM +0530, 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. > 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<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<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 > -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
