[gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors
mrshirts at gmail.com
Thu Jul 18 05:30:32 CEST 2013
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 working on checking various combinations of expanded ensemble and
integrators that can more easily be supported, but that may take a few
On Wed, Jul 17, 2013 at 6:22 PM, Dejun Lin <dejun.lin at gmail.com> wrote:
> 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.
>> > I ran the tutorial on
>> > 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
>> > 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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