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

Dejun Lin dejun.lin at gmail.com
Thu Jul 18 02:22:56 CEST 2013

The test I did was using gmx-4.6.3. I'm currently working on a membrane
system, which requires semiisotropic pressure coupling. I know that MTTK in
gmx-4.6.3 doesn't support semiiso yet so the only combination available for
expanded ensemble is md-vv + v-rescale tcoupl + berendsen pcoupl, which I'm
testing right now. A preliminary run gave me some sane dG values although
it's not optimal for data collection as you pointed out. I wonder if it's a
trivial fix that might have been done to add semiiso to MTTK?

Thanks again for your help!

2013/7/17 Michael Shirts <mrshirts at gmail.com>

> > It seems to have something to do with the integrator/pressure-coupling.
> that is what I expected based on some preliminary testing earlier.
> When
> > I ran the tutorial on
> >
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble
> ,
> > everything seems fine
> OK good!
> > unless I switched to sd integrator instead of md-vv
> There may be a problem with sd and expanded ensemble. This MAY have
> been fixed in 4.6.3, but I'll need a little bit of time to check.
> > (and Pcoupl from MTTK to berendsen),
> Berendsen is provably wrong. The ensemble is incorrect.  It is evil
> whenever a true distribution is needed. There are warnings that should
> be printed when you set up the system.  Perhaps they should be made
> stronger with expanded ensemble!
> in which case SHAKE didn't seem to be
> > able to settle the constraints.
> Expanded ensemble is rough on constraints.  The integration is
> formally correct, but it is harder to converge pressure, especially
> with constraints.  The larger the system, however, the more stable it
> is.
> > file from the tutorial. Any idea?
> Well, one solution is to run your molecule with the parameters in the
> .mdp!  Would that solve your problem for now?
> Longer term. I will check on the SD to see if it is fixed in 4.6.3 --
> I seem to re call this, but I'm not sure.   However, I am not sure
> that it can be made formally correct.  I will either fix this or make
> the warnings more clear -- or not permit it at all.
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