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

[Michael Shirts]

> 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.