[gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

[Dejun Lin]

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 <mrshirts at 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.lin at 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.
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