The following manuscript may be of interest. http://arxiv.org/abs/math/0610124v2
-Robert McGibbon On Apr 5, 2012, at 11:26 AM, Acoot Brett wrote: > But we hope finally no matter which trajectory, a stable protein conformation > should be got! As for during the production MD, no significant energy change > included. > > I am looking forward to getting more feedback on this topic. > > Acoot > > From: Peter C. Lai <p...@uab.edu> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Friday, 6 April 2012 4:20 AM > Subject: Re: [gmx-users] Different results from identical tpr after MD > > 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 > > > -- > 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
