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
