On 6/04/2012 3:53 PM, bipin singh wrote:
Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such research article then please send me the link.
Doubtless there are others, but Tsjerk's http://dx.doi.org/10.1021/jp068580v is a good start.
Mark
On Thu, Apr 5, 2012 at 23:50, Peter C. Lai <p...@uab.edu <mailto:p...@uab.edu>> wrote: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 <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> > > > > -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> > > > > ==============================**========== > > -- > > 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> > > 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 <mailto: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 <mailto: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 <mailto: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 <mailto:p...@uab.edu> | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org <mailto: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 <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ----------------------- /Thanks and Regards,/ Bipin Singh
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