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 weeks. On Wed, Jul 17, 2013 at 6:22 PM, Dejun Lin <dejun....@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 <mrshi...@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. >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
