Unfortunately, the semiiso fix for MTTK is not trivial, and will have
to wait until 5.0.
Berendsen volume + expanded ensemble would likely give very bad
results, especially since surface area fluctuations are important.
Replica exchange works with sd and parrinello-Rahman, if that helps!
I am wo
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
> 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 go
That's a good question. My understanding and experience is the
difference in required overlap in replica exchange and expanded
ensemble methods is not significant. There are probably some more
detailed studies out there. Expanded ensemble can be somewhat more
efficient (see a paper by Park and Pa
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 lambd
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
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