Thanks Justin for the Quick and Helpful reply. Yes. If I am right, the chaotic behavior of the simulations is inherent and can be assessed statistically by generating several independent trajectories and analyzing their similar outcomes. But with the same '.mdp' file I am getting TOO much different results, and that's where I worry. I'll surely try with the recent version of gromacs. But, for now, can you give me a little more informations about problems (bugs) with the 4.5.5 version, related to my context?
Tarak On Sun, May 12, 2013 at 10:55 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/12/13 1:17 PM, tarak karmakar wrote: > >> Dear All, >> >> I am simulating a protein in water to check the ligand movement >> over a >> time span. I have minimized the system in STEEP and CG and after that >> heated from 0K - 300K within a time span of 300 ps. Then, I performed the >> NPT production runs. In two clusters I have got different results, like in >> one I see the ligand came out of the protein and in other it stayed inside >> the protein cavity, after a same (comparable) time duration. Now, while >> running the same job (same .mdp file) in different numbers of cores (in >> the >> same machine) I'm getting different behaviors, e.g., in protein ligand >> distance plots etc. I don't know the reason behind this. I'm running all >> my >> jobs in gromacs-4.5.5 version. >> Recently I have visited this post [ >> http://redmine.gromacs.org/**issues/1012<http://redmine.gromacs.org/issues/1012>], >> but could not able to conclude >> properly. Anyone's help would be greatly appreciated. >> >> > I don't know if that issue is related, but if it is, then you're using an > affected version (4.5.5). Run again using the latest version (4.6.1) and > see if the problem persists. Realize too that MD simulations are chaotic, > and there is no guarantee that one trajectory will be identical to another. > In principal, on average, multiple trajectories should produce similar > behavior. If you think that core count is a problem, run with mdrun > -reprod to see if any optimizations are causing issues. Build a solid test > case, one that eliminates the possibility that your ligand topology is > inaccurate. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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> > * * -- 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
