> 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
