I can't think of any instance where nose-hoover chains provides an advantage over nose-hoover in a large system -- all the demonstrations of superiority are in model systems that are not particularly chaotic. As the system gets more chaotic, it matters less.
I would go with md, nose-hoover (w/o chains), and Parrinello-Rahman with semiisotropic scaling. On Sat, Jun 1, 2013 at 1:07 AM, James Starlight <jmsstarli...@gmail.com> wrote: > Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK > barostat 5ps coupling ) I've observed non-physical behaviour of my system > with the constant drift of the protein molecule as the rigid body in the > y-z plane > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Pressure -760.137 -- 193.776 218.059 (bar) > > > >From manual I've noticed that MMTK doest not support *semiisotropic > scalling. *Doest it means that with the Nose-hover chains and md-vv I > should use only weaker coupling during productions runs (I cant use > Parinello;s barostat with such options too) > > Thanks for help > > James > > > > 2013/5/31 James Starlight <jmsstarli...@gmail.com> > >> Dear Gromacs users! >> >> I'd like to perform simulation of the membrane protein in lipid-water >> system using Nose-Hover with chains. >> >> From manual I've found that with such thermostat I should use (1) md-vv >> integrator (2) MTTK instead of Parinello's batostat and (3) shake instead >> of LINCS. >> >> >> How doest such options compatible with the simulation of membrane proteins >> in general ? On what other options should I pay attention during simulation >> of membrane protein with NH chains ? >> >> >> >> Thanks for help, >> James >> > -- > 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
