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
