And I my point was I didn't think that there was going to be a measurable ergodicity difference between NH chains and NH. Given the size of the system, the chaoticness of atomic motions will likely give you configurational sampling indistinguishable from full ergodicity. Most of the errors that are solved by NH chains are for small toy systems.
On Sun, Jun 2, 2013 at 2:17 AM, James Starlight <jmsstarli...@gmail.com> wrote: > Michael, > > > thanks for suggestions. > > the main reason of ussage N-H with chains is the assumption that simple N-H > does not provide ergodicity of the system assuming that I'd like to sample > all temperature acceptable conformations on the 100 ns trajectory. > > But as I understood the chain regime does not compatible with the membrane > protein simulation due to the artifacts arising with MTTK batostat. > > James > > 2013/6/1 Michael Shirts <mrshi...@gmail.com> > >> 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 >> > -- > 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
