Hi Michael, Thanks for the reply. Just a quick follow-up. Do you think the overlap of energy histogram between different lambdas matter for lambda-dynamics in general? (Maybe not in this particular case or in the case of the tutorial you just posted.) I wonder if we need as many intermediate lambdas as in the case of replica exchange since the weights compensate the difference in energy.
Thanks, Dejun 2013/7/16 Michael Shirts <mrshi...@gmail.com> > Hi, all- > > This not a problem with W-L, but is instead something that is wrong > with a particular combination of mdp options that are not working for > expanded ensemble simulations. W-L can equilibrate to incorrect > distributions because it decreases the weights too fast (more on that > later), but that is not the problem here. The option wl-oneovert > allows switching to a slower scaling that is more likely to converge. > > The reason that it is not a W-L problem is that after the WL weights > are equilibrated, it is equilibrium sampling in the expanded ensemble. > If the W-L equilibration was a problem, then the distribution of > states would not be flat. They are flat, so therefore the expanded > ensemble dynamics are wrong. > > I have example expanded ensemble setups. > > > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble > > These mdp files should work. Note that you should be able to swap out > any top, and it will still work. If you get CORRECT results (and it > should take just a few ns to see) with these tops, then I will go > through and try to figure out which differences are causing the > problems. > > Thanks for the patience while we test this new functionality. > Frequently when one puts new code in the hands of others it breaks in > ways that were not foreseen! > > On Tue, Jul 16, 2013 at 12:53 PM, Dejun Lin <dejun....@gmail.com> wrote: > > I have a similar question here. Can anyone tell if the Wang-Landau > algorithm > > in lambda space is robust in that it doesn't depend on the choice of the > > convergence factor (weight-equil-wl-delta), the flatness of the histogram > > (wl-ratio) and/or the frequency of trial move (nstexpanded), especially > in > > the case of barely overlapping energy distribution corresponding to > > different lambdas? I can imagine in the extreme case, with only 2 > lambdas ( > > l = 1 or 0), the gap between the 2 energy distributions might be so large > > such that for most of the time, trial moves from the "center" of > > distribution 1 would frequently end up in the "tail" of distribution 0. > In > > this case, the Wang-Landau weights would be biased if there's not enough > > time for the system to relax back to equilibrium. > > > > Thanks, > > Dejun > > > > > > > > -- > > View this message in context: > http://gromacs.5086.x6.nabble.com/gmx-4-6-1-Expanded-ensemble-weird-balancing-factors-tp5007681p5009892.html > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > -- > > 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
