Thanks. http://redmine.gromacs.org/issues/1053 created.
Mark On Fri, Nov 30, 2012 at 5:16 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/30/12 11:00 AM, Mark Abraham wrote: > >> On Fri, Nov 30, 2012 at 2:35 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 11/30/12 8:21 AM, escajarro wrote: >>> >>> I do have constraints, all the bond lengths are fixed and they are >>>> specified >>>> in the topology file. Am I doing something wrong? I copy here the >>>> definition >>>> of one of the models I use. I also tried using in the input the line: >>>> >>>> constraints = all-bonds >>>> >>>> instead of >>>> >>>> constraints = none >>>> >>>> with the same result >>>> >>>> <http://gromacs.5086.n6.**nabb**le.com/file/n5003394/****Clipboard.jpg<http://nabble.com/file/n5003394/**Clipboard.jpg> >>>> <http://gromacs.**5086.n6.nabble.com/file/**n5003394/Clipboard.jpg<http://gromacs.5086.n6.nabble.com/file/n5003394/Clipboard.jpg> >>>> > >>>> >>>>> >>>>> >>>> >>>> >>>> That all looks fine, and the results should be the same under those two >>> circumstances. The problem is likely due to the fact that L-BFGS cannot >>> actually make use of constraints (a bug in mdrun), so that is the source >>> of >>> the difference. The EM is being done without constraints, and then the >>> MD >>> starts with constraints. Use a different EM algorithm and see if the >>> outcome improves. >>> >> >> >> If L-BFGS is silently not using the constraints, then I think that is a >> real bug and it would be good to report it so we might sometime fix it. Or >> maybe it's an undocumented "feature" we need to document? Which is it, >> please? >> >> > From the recent discussion, it seems that L-BFGS is silently ignoring the > constraints, as Berk observed there is no check for this combination, which > explained David's finding that bond lengths seem to vary randomly: > > http://lists.gromacs.org/**pipermail/gmx-developers/2012-** > November/006433.html<http://lists.gromacs.org/pipermail/gmx-developers/2012-November/006433.html> > > > -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 [email protected] > 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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
